Error in QAReport function of package affyQCReport
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Mark W Kimpel ▴ 830
@mark-w-kimpel-2027
Last seen 6.6 years ago
I am running into an error when I run QAReport on an affybatch object. Below is my sessionInfo and output. I am using the devel versions of R and BioC, all newly updated. Please advise. Thanks, Mark Browse[1]> sessionInfo() R version 2.6.0 Under development (unstable) (2007-06-30 r42095) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US. UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8 ;LC_IDENTIFICATION=C attached base packages: [1] grDevices datasets splines graphics stats tools utils [8] methods base other attached packages: [1] hgu95av2cdf_1.17.0 rat2302cdf_1.17.0 affyQCReport_1.15.2 [4] geneplotter_1.15.2 lattice_0.16-2 RColorBrewer_1.0-1 [7] affyPLM_1.13.6 affydata_1.11.2 simpleaffy_2.11.21 [10] affycoretools_1.9.2 annaffy_1.9.1 xtable_1.4-6 [13] gcrma_2.9.1 matchprobes_1.9.10 biomaRt_1.11.4 [16] RCurl_0.8-1 XML_1.9-0 GOstats_2.3.8 [19] Category_2.3.16 genefilter_1.15.3 survival_2.32 [22] KEGG_1.17.0 RBGL_1.13.3 annotate_1.15.2 [25] AnnotationDbi_0.0.83 RSQLite_0.6-0 DBI_0.2-3 [28] GO_1.17.0 graph_1.15.10 limma_2.11.9 [31] affy_1.15.7 preprocessCore_0.99.12 affyio_1.5.6 [34] Biobase_1.15.21 loaded via a namespace (and not attached): [1] cluster_1.11.7 grid_2.6.0 KernSmooth_2.22-20 > affy.batch.sub AffyBatch object size of arrays=834x834 features (14 kb) cdf=Rat230_2 (31099 affyids) number of samples=16 number of genes=31099 annotation=rat2302 notes= > QCReport(affy.batch.sub) Error in attr(groups, "names") <- names : 'names' attribute [16] must be the same length as the vector [1] Enter a frame number, or 0 to exit 1: QCReport(affy.batch.sub) 2: signalDist(object) 3: boxplot(object, names = ArrayIndex, ylab = "Log2(Intensity)", xlab = "Array 4: boxplot.default(object, names = ArrayIndex, ylab = "Log2(Intensity)", xlab Selection: 4 Called from: eval(expr, envir, enclos) Browse[1]> ls() [1] "add" "args" "at" "border" "col" [6] "groups" "horizontal" "log" "n" "namedargs" [11] "names" "notch" "outline" "pars" "plot" [16] "range" "*tmp*" "varwidth" "width" "x" Browse[1]> names [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" "14" "15" [16] "16" Browse[1]> names(group) NULL Browse[1]> names(groups) [1] "" Browse[1]> names(groups) <- names Error during wrapup: 'names' attribute [16] must be the same length as the vector [1] Browse[1]> -- --- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please) ******************************************************************
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Mark W Kimpel ▴ 830
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I am running into an error when I run QAReport on an affybatch object. Below is my sessionInfo and output. I am using the devel versions of R and BioC, all newly updated. Please advise. Thanks, Mark Browse[1]> sessionInfo() R version 2.6.0 Under development (unstable) (2007-06-30 r42095) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US. UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8 ;LC_IDENTIFICATION=C attached base packages: [1] grDevices datasets splines graphics stats tools utils [8] methods base other attached packages: [1] hgu95av2cdf_1.17.0 rat2302cdf_1.17.0 affyQCReport_1.15.2 [4] geneplotter_1.15.2 lattice_0.16-2 RColorBrewer_1.0-1 [7] affyPLM_1.13.6 affydata_1.11.2 simpleaffy_2.11.21 [10] affycoretools_1.9.2 annaffy_1.9.1 xtable_1.4-6 [13] gcrma_2.9.1 matchprobes_1.9.10 biomaRt_1.11.4 [16] RCurl_0.8-1 XML_1.9-0 GOstats_2.3.8 [19] Category_2.3.16 genefilter_1.15.3 survival_2.32 [22] KEGG_1.17.0 RBGL_1.13.3 annotate_1.15.2 [25] AnnotationDbi_0.0.83 RSQLite_0.6-0 DBI_0.2-3 [28] GO_1.17.0 graph_1.15.10 limma_2.11.9 [31] affy_1.15.7 preprocessCore_0.99.12 affyio_1.5.6 [34] Biobase_1.15.21 loaded via a namespace (and not attached): [1] cluster_1.11.7 grid_2.6.0 KernSmooth_2.22-20 > affy.batch.sub AffyBatch object size of arrays=834x834 features (14 kb) cdf=Rat230_2 (31099 affyids) number of samples=16 number of genes=31099 annotation=rat2302 notes= > QCReport(affy.batch.sub) Error in attr(groups, "names") <- names : 'names' attribute [16] must be the same length as the vector [1] Enter a frame number, or 0 to exit 1: QCReport(affy.batch.sub) 2: signalDist(object) 3: boxplot(object, names = ArrayIndex, ylab = "Log2(Intensity)", xlab = "Array 4: boxplot.default(object, names = ArrayIndex, ylab = "Log2(Intensity)", xlab Selection: 4 Called from: eval(expr, envir, enclos) Browse[1]> ls() [1] "add" "args" "at" "border" "col" [6] "groups" "horizontal" "log" "n" "namedargs" [11] "names" "notch" "outline" "pars" "plot" [16] "range" "*tmp*" "varwidth" "width" "x" Browse[1]> names [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" "14" "15" [16] "16" Browse[1]> names(group) NULL Browse[1]> names(groups) [1] "" Browse[1]> names(groups) <- names Error during wrapup: 'names' attribute [16] must be the same length as the vector [1] Browse[1]> -- --- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please)
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It looks to me like you are using a function named QCReport, not QAReport (and indeed there is no such thing - you might look at affyQAReport, which is in the same package but is very different). You can try to see what is happening by looking at the code from signalDist: par(mfrow=c(2, 1)) ArrayIndex = as.character(1:length(sampleNames(object))) boxplot(object,names=ArrayIndex,ylab="Log2(Intensity)",xlab="Array Index") where instead of object you use affy.batch.sub. The code looks pretty straightforward, so I don't know what the problem might be. It is a bit odd, it seems to me to use integers in place of the sample names... I used the affybatch.example and it worked for me.. ( one issue with that was Warning message: In data.row.names(row.names, rowsi, i) : some row.names duplicated: 2,26,51,76,101,126,151,176,201,226,251,276,301,326,351,376,401,426,451 ,476,501,526,551,576,601,626,651,676,701,726,751,776,801,826, ... which we may need to look at). best wishes Robert Mark W Kimpel wrote: > I am running into an error when I run QAReport on an affybatch object. > Below is my sessionInfo and output. I am using the devel versions of R > and BioC, all newly updated. Please advise. > > Thanks, > Mark > > Browse[1]> sessionInfo() > R version 2.6.0 Under development (unstable) (2007-06-30 r42095) > i686-pc-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_U S.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF -8;LC_IDENTIFICATION=C > > attached base packages: > [1] grDevices datasets splines graphics stats tools utils > [8] methods base > > other attached packages: > [1] hgu95av2cdf_1.17.0 rat2302cdf_1.17.0 affyQCReport_1.15.2 > [4] geneplotter_1.15.2 lattice_0.16-2 RColorBrewer_1.0-1 > [7] affyPLM_1.13.6 affydata_1.11.2 simpleaffy_2.11.21 > [10] affycoretools_1.9.2 annaffy_1.9.1 xtable_1.4-6 > [13] gcrma_2.9.1 matchprobes_1.9.10 biomaRt_1.11.4 > [16] RCurl_0.8-1 XML_1.9-0 GOstats_2.3.8 > [19] Category_2.3.16 genefilter_1.15.3 survival_2.32 > [22] KEGG_1.17.0 RBGL_1.13.3 annotate_1.15.2 > [25] AnnotationDbi_0.0.83 RSQLite_0.6-0 DBI_0.2-3 > [28] GO_1.17.0 graph_1.15.10 limma_2.11.9 > [31] affy_1.15.7 preprocessCore_0.99.12 affyio_1.5.6 > [34] Biobase_1.15.21 > > loaded via a namespace (and not attached): > [1] cluster_1.11.7 grid_2.6.0 KernSmooth_2.22-20 > > > affy.batch.sub > AffyBatch object > size of arrays=834x834 features (14 kb) > cdf=Rat230_2 (31099 affyids) > number of samples=16 > number of genes=31099 > annotation=rat2302 > notes= > > QCReport(affy.batch.sub) > Error in attr(groups, "names") <- names : > 'names' attribute [16] must be the same length as the vector [1] > > Enter a frame number, or 0 to exit > > 1: QCReport(affy.batch.sub) > 2: signalDist(object) > 3: boxplot(object, names = ArrayIndex, ylab = "Log2(Intensity)", xlab = > "Array > 4: boxplot.default(object, names = ArrayIndex, ylab = "Log2(Intensity)", > xlab > > Selection: 4 > Called from: eval(expr, envir, enclos) > Browse[1]> ls() > [1] "add" "args" "at" "border" "col" > [6] "groups" "horizontal" "log" "n" "namedargs" > [11] "names" "notch" "outline" "pars" "plot" > [16] "range" "*tmp*" "varwidth" "width" "x" > Browse[1]> names > [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" > "14" "15" > [16] "16" > Browse[1]> names(group) > NULL > Browse[1]> names(groups) > [1] "" > Browse[1]> names(groups) <- names > Error during wrapup: 'names' attribute [16] must be the same length as > the vector [1] > Browse[1]> -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org
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Robert, You are correct, I am using the function QCReport. I downloaded the source code of the packages affy and affyQCReport and believe the problem may be that the wrong method is being called when boxplot is invoked on my affybatch object. I get an error when I do signature(affy.batch). See below... Is this expected behavior? Could my affybatch object be corrupted? Mark > signature(affy.batch) Error in signature(affy.batch) : bad class specified for element 1 (should be a single character string) Enter a frame number, or 0 to exit 1: signature(affy.batch) Selection: 1 Called from: eval(expr, envir, enclos) Browse[1]> ls() [1] "i" "names" "sigi" "value" Browse[1]> value [[1]] AffyBatch object size of arrays=834x834 features (23 kb) cdf=Rat230_2 (31099 affyids) number of samples=80 number of genes=31099 annotation=rat2302 notes= Browse[1]> i [1] 1 Browse[1]> names NULL Browse[1]> sigi AffyBatch object size of arrays=834x834 features (23 kb) cdf=Rat230_2 (31099 affyids) number of samples=80 number of genes=31099 annotation=rat2302 notes= Browse[1]> Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please) ****************************************************************** Robert Gentleman wrote: > It looks to me like you are using a function named QCReport, not > QAReport (and indeed there is no such thing - you might look at > affyQAReport, which is in the same package but is very different). > > You can try to see what is happening by looking at the code from > signalDist: > > par(mfrow=c(2, 1)) > ArrayIndex = as.character(1:length(sampleNames(object))) > boxplot(object,names=ArrayIndex,ylab="Log2(Intensity)",xlab="Array Index") > > > where instead of object you use affy.batch.sub. The code looks pretty > straightforward, so I don't know what the problem might be. It is a bit > odd, it seems to me to use integers in place of the sample names... > > I used the affybatch.example and it worked for me.. ( one issue with > that was > Warning message: > In data.row.names(row.names, rowsi, i) : > some row.names duplicated: > 2,26,51,76,101,126,151,176,201,226,251,276,301,326,351,376,401,426,4 51,476,501,526,551,576,601,626,651,676,701,726,751,776,801,826, > > .... > > which we may need to look at). > > best wishes > Robert > > > Mark W Kimpel wrote: >> I am running into an error when I run QAReport on an affybatch object. >> Below is my sessionInfo and output. I am using the devel versions of R >> and BioC, all newly updated. Please advise. >> >> Thanks, >> Mark >> >> Browse[1]> sessionInfo() >> R version 2.6.0 Under development (unstable) (2007-06-30 r42095) >> i686-pc-linux-gnu >> >> locale: >> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en _US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_ US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UT F-8;LC_IDENTIFICATION=C >> >> >> attached base packages: >> [1] grDevices datasets splines graphics stats tools utils >> [8] methods base >> >> other attached packages: >> [1] hgu95av2cdf_1.17.0 rat2302cdf_1.17.0 affyQCReport_1.15.2 >> [4] geneplotter_1.15.2 lattice_0.16-2 RColorBrewer_1.0-1 >> [7] affyPLM_1.13.6 affydata_1.11.2 simpleaffy_2.11.21 >> [10] affycoretools_1.9.2 annaffy_1.9.1 xtable_1.4-6 >> [13] gcrma_2.9.1 matchprobes_1.9.10 biomaRt_1.11.4 >> [16] RCurl_0.8-1 XML_1.9-0 GOstats_2.3.8 >> [19] Category_2.3.16 genefilter_1.15.3 survival_2.32 >> [22] KEGG_1.17.0 RBGL_1.13.3 annotate_1.15.2 >> [25] AnnotationDbi_0.0.83 RSQLite_0.6-0 DBI_0.2-3 >> [28] GO_1.17.0 graph_1.15.10 limma_2.11.9 >> [31] affy_1.15.7 preprocessCore_0.99.12 affyio_1.5.6 >> [34] Biobase_1.15.21 >> >> loaded via a namespace (and not attached): >> [1] cluster_1.11.7 grid_2.6.0 KernSmooth_2.22-20 >> >> > affy.batch.sub >> AffyBatch object >> size of arrays=834x834 features (14 kb) >> cdf=Rat230_2 (31099 affyids) >> number of samples=16 >> number of genes=31099 >> annotation=rat2302 >> notes= >> > QCReport(affy.batch.sub) >> Error in attr(groups, "names") <- names : >> 'names' attribute [16] must be the same length as the vector [1] >> >> Enter a frame number, or 0 to exit >> >> 1: QCReport(affy.batch.sub) >> 2: signalDist(object) >> 3: boxplot(object, names = ArrayIndex, ylab = "Log2(Intensity)", xlab >> = "Array >> 4: boxplot.default(object, names = ArrayIndex, ylab = >> "Log2(Intensity)", xlab >> >> Selection: 4 >> Called from: eval(expr, envir, enclos) >> Browse[1]> ls() >> [1] "add" "args" "at" "border" "col" >> [6] "groups" "horizontal" "log" "n" "namedargs" >> [11] "names" "notch" "outline" "pars" "plot" >> [16] "range" "*tmp*" "varwidth" "width" "x" >> Browse[1]> names >> [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" >> "14" "15" >> [16] "16" >> Browse[1]> names(group) >> NULL >> Browse[1]> names(groups) >> [1] "" >> Browse[1]> names(groups) <- names >> Error during wrapup: 'names' attribute [16] must be the same length as >> the vector [1] >> Browse[1]> >
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Mark W Kimpel wrote: > Robert, > > You are correct, I am using the function QCReport. I downloaded the > source code of the packages affy and affyQCReport and believe the > problem may be that the wrong method is being called when boxplot is > invoked on my affybatch object. I get an error when I do > signature(affy.batch). See below... Is this expected behavior? Could my > affybatch object be corrupted? Mark It could well be, but that is not what signature is for. You want class(affy.batch) - but you were using a subset of that I thought. It is possible to get both corrupted objects (especially if they are old and may have been created with a previous version of R) and also method dispatch can get confused. I cannot tell from what you have sent which is like to be your problem. Please check the class of the object, and also run the code I sent in the previous email with all output, that might help to figure out just what your problem is. It might also help to see the output of search and potentially of showMethods. I get: > showMethods("boxplot") Function: boxplot (package graphics) x="ANY" x="AffyBatch" with the affy package attached. best wishes Robert > > > signature(affy.batch) > Error in signature(affy.batch) : > bad class specified for element 1 (should be a single character string) > > Enter a frame number, or 0 to exit > > 1: signature(affy.batch) > > Selection: 1 > Called from: eval(expr, envir, enclos) > Browse[1]> ls() > [1] "i" "names" "sigi" "value" > Browse[1]> value > [[1]] > AffyBatch object > size of arrays=834x834 features (23 kb) > cdf=Rat230_2 (31099 affyids) > number of samples=80 > number of genes=31099 > annotation=rat2302 > notes= > > Browse[1]> i > [1] 1 > Browse[1]> names > NULL > Browse[1]> sigi > AffyBatch object > size of arrays=834x834 features (23 kb) > cdf=Rat230_2 (31099 affyids) > number of samples=80 > number of genes=31099 > annotation=rat2302 > notes= > Browse[1]> > > Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry > Indiana University School of Medicine > > 15032 Hunter Court, Westfield, IN 46074 > > (317) 490-5129 Work, & Mobile & VoiceMail > (317) 663-0513 Home (no voice mail please) > > ****************************************************************** > > Robert Gentleman wrote: >> It looks to me like you are using a function named QCReport, not >> QAReport (and indeed there is no such thing - you might look at >> affyQAReport, which is in the same package but is very different). >> >> You can try to see what is happening by looking at the code from >> signalDist: >> >> par(mfrow=c(2, 1)) >> ArrayIndex = as.character(1:length(sampleNames(object))) >> boxplot(object,names=ArrayIndex,ylab="Log2(Intensity)",xlab="Array >> Index") >> >> >> where instead of object you use affy.batch.sub. The code looks pretty >> straightforward, so I don't know what the problem might be. It is a >> bit odd, it seems to me to use integers in place of the sample names... >> >> I used the affybatch.example and it worked for me.. ( one issue with >> that was >> Warning message: >> In data.row.names(row.names, rowsi, i) : >> some row.names duplicated: >> 2,26,51,76,101,126,151,176,201,226,251,276,301,326,351,376,401,426, 451,476,501,526,551,576,601,626,651,676,701,726,751,776,801,826, >> >> .... >> >> which we may need to look at). >> >> best wishes >> Robert >> >> >> Mark W Kimpel wrote: >>> I am running into an error when I run QAReport on an affybatch >>> object. Below is my sessionInfo and output. I am using the devel >>> versions of R and BioC, all newly updated. Please advise. >>> >>> Thanks, >>> Mark >>> >>> Browse[1]> sessionInfo() >>> R version 2.6.0 Under development (unstable) (2007-06-30 r42095) >>> i686-pc-linux-gnu >>> >>> locale: >>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=e n_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en _US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.U TF-8;LC_IDENTIFICATION=C >>> >>> >>> attached base packages: >>> [1] grDevices datasets splines graphics stats tools utils >>> [8] methods base >>> >>> other attached packages: >>> [1] hgu95av2cdf_1.17.0 rat2302cdf_1.17.0 affyQCReport_1.15.2 >>> [4] geneplotter_1.15.2 lattice_0.16-2 RColorBrewer_1.0-1 >>> [7] affyPLM_1.13.6 affydata_1.11.2 simpleaffy_2.11.21 >>> [10] affycoretools_1.9.2 annaffy_1.9.1 xtable_1.4-6 >>> [13] gcrma_2.9.1 matchprobes_1.9.10 biomaRt_1.11.4 >>> [16] RCurl_0.8-1 XML_1.9-0 GOstats_2.3.8 >>> [19] Category_2.3.16 genefilter_1.15.3 survival_2.32 >>> [22] KEGG_1.17.0 RBGL_1.13.3 annotate_1.15.2 >>> [25] AnnotationDbi_0.0.83 RSQLite_0.6-0 DBI_0.2-3 >>> [28] GO_1.17.0 graph_1.15.10 limma_2.11.9 >>> [31] affy_1.15.7 preprocessCore_0.99.12 affyio_1.5.6 >>> [34] Biobase_1.15.21 >>> >>> loaded via a namespace (and not attached): >>> [1] cluster_1.11.7 grid_2.6.0 KernSmooth_2.22-20 >>> >>> > affy.batch.sub >>> AffyBatch object >>> size of arrays=834x834 features (14 kb) >>> cdf=Rat230_2 (31099 affyids) >>> number of samples=16 >>> number of genes=31099 >>> annotation=rat2302 >>> notes= >>> > QCReport(affy.batch.sub) >>> Error in attr(groups, "names") <- names : >>> 'names' attribute [16] must be the same length as the vector [1] >>> >>> Enter a frame number, or 0 to exit >>> >>> 1: QCReport(affy.batch.sub) >>> 2: signalDist(object) >>> 3: boxplot(object, names = ArrayIndex, ylab = "Log2(Intensity)", xlab >>> = "Array >>> 4: boxplot.default(object, names = ArrayIndex, ylab = >>> "Log2(Intensity)", xlab >>> >>> Selection: 4 >>> Called from: eval(expr, envir, enclos) >>> Browse[1]> ls() >>> [1] "add" "args" "at" "border" "col" >>> [6] "groups" "horizontal" "log" "n" "namedargs" >>> [11] "names" "notch" "outline" "pars" "plot" >>> [16] "range" "*tmp*" "varwidth" "width" "x" >>> Browse[1]> names >>> [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" >>> "13" "14" "15" >>> [16] "16" >>> Browse[1]> names(group) >>> NULL >>> Browse[1]> names(groups) >>> [1] "" >>> Browse[1]> names(groups) <- names >>> Error during wrapup: 'names' attribute [16] must be the same length >>> as the vector [1] >>> Browse[1]> >> > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org
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Dear list, I am looking for a function to compare lists of GO terms, e.g. compute semantic similarity or the minimum common graph, etc, that works with GO ids... I looked into the GO packages at Bioconductor but it seems to me that functions to perform such comparisons only accept as input list of gene IDs, and not GO IDs. Am I right/wrong? Any help appreciated Cheers Ana
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Seth and Robert, Looks like I may have more than one problem. To clarify one point first, in my original post I was using affy.batch.sub, which consisted of just some of the arrays from my affy.batch. To make sure I'm not having a problem with subsetting, in my subsequent posts I am using the affybatch object created just today with ReadAffy. No old versions here, just what comes out of my sessionInfo(). As you can see below, there may be a problem with my boxplot method but also with the affybatch object. The latter is of class AffyBatch but is not a valid object. Thanks, Mark > class(affy.batch) [1] "AffyBatch" attr(,"package") [1] "affy" > require(affy) > showMethods("boxplot") Error in get(if (inherited) ".AllMTable" else ".MTable", envir = env) : variable ".AllMTable" was not found Enter a frame number, or 0 to exit 1: showMethods("boxplot") 2: .showMethodsTable(getGeneric(f, where = where), includeDefs, inherited, cla 3: get(if (inherited) ".AllMTable" else ".MTable", envir = env) > validObject(affy.batch) Error in validObject(affy.batch) : invalid class "AffyBatch" object: sampleNames differ between assayData and phenoData Enter a frame number, or 0 to exit 1: validObject(affy.batch) > par(mfrow=c(2, 1)) > ArrayIndex = as.character(1:length(sampleNames(affy.batch))) > boxplot(affy.batch,names=ArrayIndex,ylab="Log2(Intensity)",xlab="Array Index") Error in attr(groups, "names") <- names : 'names' attribute [80] must be the same length as the vector [1] Enter a frame number, or 0 to exit 1: boxplot(affy.batch, names = ArrayIndex, ylab = "Log2(Intensity)", xlab = "A 2: boxplot(affy.batch, names = ArrayIndex, ylab = "Log2(Intensity)", xlab = "A 3: boxplot.default(affy.batch, names = ArrayIndex, ylab = "Log2(Intensity)", x Selection: --- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please) ****************************************************************** Robert Gentleman wrote: > It looks to me like you are using a function named QCReport, not > QAReport (and indeed there is no such thing - you might look at > affyQAReport, which is in the same package but is very different). > > You can try to see what is happening by looking at the code from > signalDist: > > par(mfrow=c(2, 1)) > ArrayIndex = as.character(1:length(sampleNames(object))) > boxplot(object,names=ArrayIndex,ylab="Log2(Intensity)",xlab="Array Index") > > > where instead of object you use affy.batch.sub. The code looks pretty > straightforward, so I don't know what the problem might be. It is a bit > odd, it seems to me to use integers in place of the sample names... > > I used the affybatch.example and it worked for me.. ( one issue with > that was > Warning message: > In data.row.names(row.names, rowsi, i) : > some row.names duplicated: > 2,26,51,76,101,126,151,176,201,226,251,276,301,326,351,376,401,426,4 51,476,501,526,551,576,601,626,651,676,701,726,751,776,801,826, > > .... > > which we may need to look at). > > best wishes > Robert > > > Mark W Kimpel wrote: >> I am running into an error when I run QAReport on an affybatch object. >> Below is my sessionInfo and output. I am using the devel versions of R >> and BioC, all newly updated. Please advise. >> >> Thanks, >> Mark >> >> Browse[1]> sessionInfo() >> R version 2.6.0 Under development (unstable) (2007-06-30 r42095) >> i686-pc-linux-gnu >> >> locale: >> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en _US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_ US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UT F-8;LC_IDENTIFICATION=C >> >> >> attached base packages: >> [1] grDevices datasets splines graphics stats tools utils >> [8] methods base >> >> other attached packages: >> [1] hgu95av2cdf_1.17.0 rat2302cdf_1.17.0 affyQCReport_1.15.2 >> [4] geneplotter_1.15.2 lattice_0.16-2 RColorBrewer_1.0-1 >> [7] affyPLM_1.13.6 affydata_1.11.2 simpleaffy_2.11.21 >> [10] affycoretools_1.9.2 annaffy_1.9.1 xtable_1.4-6 >> [13] gcrma_2.9.1 matchprobes_1.9.10 biomaRt_1.11.4 >> [16] RCurl_0.8-1 XML_1.9-0 GOstats_2.3.8 >> [19] Category_2.3.16 genefilter_1.15.3 survival_2.32 >> [22] KEGG_1.17.0 RBGL_1.13.3 annotate_1.15.2 >> [25] AnnotationDbi_0.0.83 RSQLite_0.6-0 DBI_0.2-3 >> [28] GO_1.17.0 graph_1.15.10 limma_2.11.9 >> [31] affy_1.15.7 preprocessCore_0.99.12 affyio_1.5.6 >> [34] Biobase_1.15.21 >> >> loaded via a namespace (and not attached): >> [1] cluster_1.11.7 grid_2.6.0 KernSmooth_2.22-20 >> >> > affy.batch.sub >> AffyBatch object >> size of arrays=834x834 features (14 kb) >> cdf=Rat230_2 (31099 affyids) >> number of samples=16 >> number of genes=31099 >> annotation=rat2302 >> notes= >> > QCReport(affy.batch.sub) >> Error in attr(groups, "names") <- names : >> 'names' attribute [16] must be the same length as the vector [1] >> >> Enter a frame number, or 0 to exit >> >> 1: QCReport(affy.batch.sub) >> 2: signalDist(object) >> 3: boxplot(object, names = ArrayIndex, ylab = "Log2(Intensity)", xlab >> = "Array >> 4: boxplot.default(object, names = ArrayIndex, ylab = >> "Log2(Intensity)", xlab >> >> Selection: 4 >> Called from: eval(expr, envir, enclos) >> Browse[1]> ls() >> [1] "add" "args" "at" "border" "col" >> [6] "groups" "horizontal" "log" "n" "namedargs" >> [11] "names" "notch" "outline" "pars" "plot" >> [16] "range" "*tmp*" "varwidth" "width" "x" >> Browse[1]> names >> [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" >> "14" "15" >> [16] "16" >> Browse[1]> names(group) >> NULL >> Browse[1]> names(groups) >> [1] "" >> Browse[1]> names(groups) <- names >> Error during wrapup: 'names' attribute [16] must be the same length as >> the vector [1] >> Browse[1]> >
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Mark W Kimpel ▴ 830
@mark-w-kimpel-2027
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I am running into an error when I run QAReport on an affybatch object. Below is my sessionInfo and output. I am using the devel versions of R and BioC, all newly updated. Please advise. Thanks, Mark Browse[1]> sessionInfo() R version 2.6.0 Under development (unstable) (2007-06-30 r42095) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US. UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8 ;LC_IDENTIFICATION=C attached base packages: [1] grDevices datasets splines graphics stats tools utils [8] methods base other attached packages: [1] hgu95av2cdf_1.17.0 rat2302cdf_1.17.0 affyQCReport_1.15.2 [4] geneplotter_1.15.2 lattice_0.16-2 RColorBrewer_1.0-1 [7] affyPLM_1.13.6 affydata_1.11.2 simpleaffy_2.11.21 [10] affycoretools_1.9.2 annaffy_1.9.1 xtable_1.4-6 [13] gcrma_2.9.1 matchprobes_1.9.10 biomaRt_1.11.4 [16] RCurl_0.8-1 XML_1.9-0 GOstats_2.3.8 [19] Category_2.3.16 genefilter_1.15.3 survival_2.32 [22] KEGG_1.17.0 RBGL_1.13.3 annotate_1.15.2 [25] AnnotationDbi_0.0.83 RSQLite_0.6-0 DBI_0.2-3 [28] GO_1.17.0 graph_1.15.10 limma_2.11.9 [31] affy_1.15.7 preprocessCore_0.99.12 affyio_1.5.6 [34] Biobase_1.15.21 loaded via a namespace (and not attached): [1] cluster_1.11.7 grid_2.6.0 KernSmooth_2.22-20 > affy.batch.sub AffyBatch object size of arrays=834x834 features (14 kb) cdf=Rat230_2 (31099 affyids) number of samples=16 number of genes=31099 annotation=rat2302 notes= > QCReport(affy.batch.sub) Error in attr(groups, "names") <- names : 'names' attribute [16] must be the same length as the vector [1] Enter a frame number, or 0 to exit 1: QCReport(affy.batch.sub) 2: signalDist(object) 3: boxplot(object, names = ArrayIndex, ylab = "Log2(Intensity)", xlab = "Array 4: boxplot.default(object, names = ArrayIndex, ylab = "Log2(Intensity)", xlab Selection: 4 Called from: eval(expr, envir, enclos) Browse[1]> ls() [1] "add" "args" "at" "border" "col" [6] "groups" "horizontal" "log" "n" "namedargs" [11] "names" "notch" "outline" "pars" "plot" [16] "range" "*tmp*" "varwidth" "width" "x" Browse[1]> names [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" "14" "15" [16] "16" Browse[1]> names(group) NULL Browse[1]> names(groups) [1] "" Browse[1]> names(groups) <- names Error during wrapup: 'names' attribute [16] must be the same length as the vector [1] Browse[1]> -- --- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please)
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It looks to me like you are using a function named QCReport, not QAReport (and indeed there is no such thing - you might look at affyQAReport, which is in the same package but is very different). You can try to see what is happening by looking at the code from signalDist: par(mfrow=c(2, 1)) ArrayIndex = as.character(1:length(sampleNames(object))) boxplot(object,names=ArrayIndex,ylab="Log2(Intensity)",xlab="Array Index") where instead of object you use affy.batch.sub. The code looks pretty straightforward, so I don't know what the problem might be. It is a bit odd, it seems to me to use integers in place of the sample names... I used the affybatch.example and it worked for me.. ( one issue with that was Warning message: In data.row.names(row.names, rowsi, i) : some row.names duplicated: 2,26,51,76,101,126,151,176,201,226,251,276,301,326,351,376,401,426,451 ,476,501,526,551,576,601,626,651,676,701,726,751,776,801,826, ... which we may need to look at). best wishes Robert Mark W Kimpel wrote: > I am running into an error when I run QAReport on an affybatch object. > Below is my sessionInfo and output. I am using the devel versions of R > and BioC, all newly updated. Please advise. > > Thanks, > Mark > > Browse[1]> sessionInfo() > R version 2.6.0 Under development (unstable) (2007-06-30 r42095) > i686-pc-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_U S.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF -8;LC_IDENTIFICATION=C > > attached base packages: > [1] grDevices datasets splines graphics stats tools utils > [8] methods base > > other attached packages: > [1] hgu95av2cdf_1.17.0 rat2302cdf_1.17.0 affyQCReport_1.15.2 > [4] geneplotter_1.15.2 lattice_0.16-2 RColorBrewer_1.0-1 > [7] affyPLM_1.13.6 affydata_1.11.2 simpleaffy_2.11.21 > [10] affycoretools_1.9.2 annaffy_1.9.1 xtable_1.4-6 > [13] gcrma_2.9.1 matchprobes_1.9.10 biomaRt_1.11.4 > [16] RCurl_0.8-1 XML_1.9-0 GOstats_2.3.8 > [19] Category_2.3.16 genefilter_1.15.3 survival_2.32 > [22] KEGG_1.17.0 RBGL_1.13.3 annotate_1.15.2 > [25] AnnotationDbi_0.0.83 RSQLite_0.6-0 DBI_0.2-3 > [28] GO_1.17.0 graph_1.15.10 limma_2.11.9 > [31] affy_1.15.7 preprocessCore_0.99.12 affyio_1.5.6 > [34] Biobase_1.15.21 > > loaded via a namespace (and not attached): > [1] cluster_1.11.7 grid_2.6.0 KernSmooth_2.22-20 > > > affy.batch.sub > AffyBatch object > size of arrays=834x834 features (14 kb) > cdf=Rat230_2 (31099 affyids) > number of samples=16 > number of genes=31099 > annotation=rat2302 > notes= > > QCReport(affy.batch.sub) > Error in attr(groups, "names") <- names : > 'names' attribute [16] must be the same length as the vector [1] > > Enter a frame number, or 0 to exit > > 1: QCReport(affy.batch.sub) > 2: signalDist(object) > 3: boxplot(object, names = ArrayIndex, ylab = "Log2(Intensity)", xlab = > "Array > 4: boxplot.default(object, names = ArrayIndex, ylab = "Log2(Intensity)", > xlab > > Selection: 4 > Called from: eval(expr, envir, enclos) > Browse[1]> ls() > [1] "add" "args" "at" "border" "col" > [6] "groups" "horizontal" "log" "n" "namedargs" > [11] "names" "notch" "outline" "pars" "plot" > [16] "range" "*tmp*" "varwidth" "width" "x" > Browse[1]> names > [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" > "14" "15" > [16] "16" > Browse[1]> names(group) > NULL > Browse[1]> names(groups) > [1] "" > Browse[1]> names(groups) <- names > Error during wrapup: 'names' attribute [16] must be the same length as > the vector [1] > Browse[1]> -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org
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Robert, You are correct, I am using the function QCReport. I downloaded the source code of the packages affy and affyQCReport and believe the problem may be that the wrong method is being called when boxplot is invoked on my affybatch object. I get an error when I do signature(affy.batch). See below... Is this expected behavior? Could my affybatch object be corrupted? Mark > signature(affy.batch) Error in signature(affy.batch) : bad class specified for element 1 (should be a single character string) Enter a frame number, or 0 to exit 1: signature(affy.batch) Selection: 1 Called from: eval(expr, envir, enclos) Browse[1]> ls() [1] "i" "names" "sigi" "value" Browse[1]> value [[1]] AffyBatch object size of arrays=834x834 features (23 kb) cdf=Rat230_2 (31099 affyids) number of samples=80 number of genes=31099 annotation=rat2302 notes= Browse[1]> i [1] 1 Browse[1]> names NULL Browse[1]> sigi AffyBatch object size of arrays=834x834 features (23 kb) cdf=Rat230_2 (31099 affyids) number of samples=80 number of genes=31099 annotation=rat2302 notes= Browse[1]> Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please) ****************************************************************** Robert Gentleman wrote: > It looks to me like you are using a function named QCReport, not > QAReport (and indeed there is no such thing - you might look at > affyQAReport, which is in the same package but is very different). > > You can try to see what is happening by looking at the code from > signalDist: > > par(mfrow=c(2, 1)) > ArrayIndex = as.character(1:length(sampleNames(object))) > boxplot(object,names=ArrayIndex,ylab="Log2(Intensity)",xlab="Array Index") > > > where instead of object you use affy.batch.sub. The code looks pretty > straightforward, so I don't know what the problem might be. It is a bit > odd, it seems to me to use integers in place of the sample names... > > I used the affybatch.example and it worked for me.. ( one issue with > that was > Warning message: > In data.row.names(row.names, rowsi, i) : > some row.names duplicated: > 2,26,51,76,101,126,151,176,201,226,251,276,301,326,351,376,401,426,4 51,476,501,526,551,576,601,626,651,676,701,726,751,776,801,826, > > .... > > which we may need to look at). > > best wishes > Robert > > > Mark W Kimpel wrote: >> I am running into an error when I run QAReport on an affybatch object. >> Below is my sessionInfo and output. I am using the devel versions of R >> and BioC, all newly updated. Please advise. >> >> Thanks, >> Mark >> >> Browse[1]> sessionInfo() >> R version 2.6.0 Under development (unstable) (2007-06-30 r42095) >> i686-pc-linux-gnu >> >> locale: >> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en _US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_ US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UT F-8;LC_IDENTIFICATION=C >> >> >> attached base packages: >> [1] grDevices datasets splines graphics stats tools utils >> [8] methods base >> >> other attached packages: >> [1] hgu95av2cdf_1.17.0 rat2302cdf_1.17.0 affyQCReport_1.15.2 >> [4] geneplotter_1.15.2 lattice_0.16-2 RColorBrewer_1.0-1 >> [7] affyPLM_1.13.6 affydata_1.11.2 simpleaffy_2.11.21 >> [10] affycoretools_1.9.2 annaffy_1.9.1 xtable_1.4-6 >> [13] gcrma_2.9.1 matchprobes_1.9.10 biomaRt_1.11.4 >> [16] RCurl_0.8-1 XML_1.9-0 GOstats_2.3.8 >> [19] Category_2.3.16 genefilter_1.15.3 survival_2.32 >> [22] KEGG_1.17.0 RBGL_1.13.3 annotate_1.15.2 >> [25] AnnotationDbi_0.0.83 RSQLite_0.6-0 DBI_0.2-3 >> [28] GO_1.17.0 graph_1.15.10 limma_2.11.9 >> [31] affy_1.15.7 preprocessCore_0.99.12 affyio_1.5.6 >> [34] Biobase_1.15.21 >> >> loaded via a namespace (and not attached): >> [1] cluster_1.11.7 grid_2.6.0 KernSmooth_2.22-20 >> >> > affy.batch.sub >> AffyBatch object >> size of arrays=834x834 features (14 kb) >> cdf=Rat230_2 (31099 affyids) >> number of samples=16 >> number of genes=31099 >> annotation=rat2302 >> notes= >> > QCReport(affy.batch.sub) >> Error in attr(groups, "names") <- names : >> 'names' attribute [16] must be the same length as the vector [1] >> >> Enter a frame number, or 0 to exit >> >> 1: QCReport(affy.batch.sub) >> 2: signalDist(object) >> 3: boxplot(object, names = ArrayIndex, ylab = "Log2(Intensity)", xlab >> = "Array >> 4: boxplot.default(object, names = ArrayIndex, ylab = >> "Log2(Intensity)", xlab >> >> Selection: 4 >> Called from: eval(expr, envir, enclos) >> Browse[1]> ls() >> [1] "add" "args" "at" "border" "col" >> [6] "groups" "horizontal" "log" "n" "namedargs" >> [11] "names" "notch" "outline" "pars" "plot" >> [16] "range" "*tmp*" "varwidth" "width" "x" >> Browse[1]> names >> [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" >> "14" "15" >> [16] "16" >> Browse[1]> names(group) >> NULL >> Browse[1]> names(groups) >> [1] "" >> Browse[1]> names(groups) <- names >> Error during wrapup: 'names' attribute [16] must be the same length as >> the vector [1] >> Browse[1]> >
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Dear list, I am looking for a function to compare lists of GO terms, e.g. compute semantic similarity or the minimum common graph, etc, that works with GO ids... I looked into the GO packages at Bioconductor but it seems to me that functions to perform such comparisons only accept as input list of gene IDs, and not GO IDs. Am I right/wrong? Any help appreciated Cheers Ana
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Seth and Robert, Looks like I may have more than one problem. To clarify one point first, in my original post I was using affy.batch.sub, which consisted of just some of the arrays from my affy.batch. To make sure I'm not having a problem with subsetting, in my subsequent posts I am using the affybatch object created just today with ReadAffy. No old versions here, just what comes out of my sessionInfo(). As you can see below, there may be a problem with my boxplot method but also with the affybatch object. The latter is of class AffyBatch but is not a valid object. Thanks, Mark > class(affy.batch) [1] "AffyBatch" attr(,"package") [1] "affy" > require(affy) > showMethods("boxplot") Error in get(if (inherited) ".AllMTable" else ".MTable", envir = env) : variable ".AllMTable" was not found Enter a frame number, or 0 to exit 1: showMethods("boxplot") 2: .showMethodsTable(getGeneric(f, where = where), includeDefs, inherited, cla 3: get(if (inherited) ".AllMTable" else ".MTable", envir = env) > validObject(affy.batch) Error in validObject(affy.batch) : invalid class "AffyBatch" object: sampleNames differ between assayData and phenoData Enter a frame number, or 0 to exit 1: validObject(affy.batch) > par(mfrow=c(2, 1)) > ArrayIndex = as.character(1:length(sampleNames(affy.batch))) > boxplot(affy.batch,names=ArrayIndex,ylab="Log2(Intensity)",xlab="Array Index") Error in attr(groups, "names") <- names : 'names' attribute [80] must be the same length as the vector [1] Enter a frame number, or 0 to exit 1: boxplot(affy.batch, names = ArrayIndex, ylab = "Log2(Intensity)", xlab = "A 2: boxplot(affy.batch, names = ArrayIndex, ylab = "Log2(Intensity)", xlab = "A 3: boxplot.default(affy.batch, names = ArrayIndex, ylab = "Log2(Intensity)", x Selection: --- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please) ****************************************************************** Robert Gentleman wrote: > It looks to me like you are using a function named QCReport, not > QAReport (and indeed there is no such thing - you might look at > affyQAReport, which is in the same package but is very different). > > You can try to see what is happening by looking at the code from > signalDist: > > par(mfrow=c(2, 1)) > ArrayIndex = as.character(1:length(sampleNames(object))) > boxplot(object,names=ArrayIndex,ylab="Log2(Intensity)",xlab="Array Index") > > > where instead of object you use affy.batch.sub. The code looks pretty > straightforward, so I don't know what the problem might be. It is a bit > odd, it seems to me to use integers in place of the sample names... > > I used the affybatch.example and it worked for me.. ( one issue with > that was > Warning message: > In data.row.names(row.names, rowsi, i) : > some row.names duplicated: > 2,26,51,76,101,126,151,176,201,226,251,276,301,326,351,376,401,426,4 51,476,501,526,551,576,601,626,651,676,701,726,751,776,801,826, > > .... > > which we may need to look at). > > best wishes > Robert > > > Mark W Kimpel wrote: >> I am running into an error when I run QAReport on an affybatch object. >> Below is my sessionInfo and output. I am using the devel versions of R >> and BioC, all newly updated. Please advise. >> >> Thanks, >> Mark >> >> Browse[1]> sessionInfo() >> R version 2.6.0 Under development (unstable) (2007-06-30 r42095) >> i686-pc-linux-gnu >> >> locale: >> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en _US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_ US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UT F-8;LC_IDENTIFICATION=C >> >> >> attached base packages: >> [1] grDevices datasets splines graphics stats tools utils >> [8] methods base >> >> other attached packages: >> [1] hgu95av2cdf_1.17.0 rat2302cdf_1.17.0 affyQCReport_1.15.2 >> [4] geneplotter_1.15.2 lattice_0.16-2 RColorBrewer_1.0-1 >> [7] affyPLM_1.13.6 affydata_1.11.2 simpleaffy_2.11.21 >> [10] affycoretools_1.9.2 annaffy_1.9.1 xtable_1.4-6 >> [13] gcrma_2.9.1 matchprobes_1.9.10 biomaRt_1.11.4 >> [16] RCurl_0.8-1 XML_1.9-0 GOstats_2.3.8 >> [19] Category_2.3.16 genefilter_1.15.3 survival_2.32 >> [22] KEGG_1.17.0 RBGL_1.13.3 annotate_1.15.2 >> [25] AnnotationDbi_0.0.83 RSQLite_0.6-0 DBI_0.2-3 >> [28] GO_1.17.0 graph_1.15.10 limma_2.11.9 >> [31] affy_1.15.7 preprocessCore_0.99.12 affyio_1.5.6 >> [34] Biobase_1.15.21 >> >> loaded via a namespace (and not attached): >> [1] cluster_1.11.7 grid_2.6.0 KernSmooth_2.22-20 >> >> > affy.batch.sub >> AffyBatch object >> size of arrays=834x834 features (14 kb) >> cdf=Rat230_2 (31099 affyids) >> number of samples=16 >> number of genes=31099 >> annotation=rat2302 >> notes= >> > QCReport(affy.batch.sub) >> Error in attr(groups, "names") <- names : >> 'names' attribute [16] must be the same length as the vector [1] >> >> Enter a frame number, or 0 to exit >> >> 1: QCReport(affy.batch.sub) >> 2: signalDist(object) >> 3: boxplot(object, names = ArrayIndex, ylab = "Log2(Intensity)", xlab >> = "Array >> 4: boxplot.default(object, names = ArrayIndex, ylab = >> "Log2(Intensity)", xlab >> >> Selection: 4 >> Called from: eval(expr, envir, enclos) >> Browse[1]> ls() >> [1] "add" "args" "at" "border" "col" >> [6] "groups" "horizontal" "log" "n" "namedargs" >> [11] "names" "notch" "outline" "pars" "plot" >> [16] "range" "*tmp*" "varwidth" "width" "x" >> Browse[1]> names >> [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" >> "14" "15" >> [16] "16" >> Browse[1]> names(group) >> NULL >> Browse[1]> names(groups) >> [1] "" >> Browse[1]> names(groups) <- names >> Error during wrapup: 'names' attribute [16] must be the same length as >> the vector [1] >> Browse[1]> >
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Hi Mark, Let's see if we cannot fix some of the problems and hopefully life will get better. Mark W Kimpel wrote: > Seth and Robert, > > Looks like I may have more than one problem. To clarify one point first, > in my original post I was using affy.batch.sub, which consisted of just > some of the arrays from my affy.batch. To make sure I'm not having a > problem with subsetting, in my subsequent posts I am using the affybatch > object created just today with ReadAffy. No old versions here, just what > comes out of my sessionInfo(). > > As you can see below, there may be a problem with my boxplot method but > also with the affybatch object. The latter is of class AffyBatch but is > not a valid object. > > Thanks, Mark > > > class(affy.batch) > [1] "AffyBatch" > attr(,"package") > [1] "affy" > > > require(affy) > > showMethods("boxplot") > Error in get(if (inherited) ".AllMTable" else ".MTable", envir = env) : > variable ".AllMTable" was not found there is something very odd about this - I have not seen it before, but it suggests that you might need to do a clean re-install of R and packages as something in the methods package (I think) is very confused. Not good news, I know, but you should not have this problem. And just to be sure this happens if you just start up R, load the affy library and then issue the commands above? That is what you need to check. Does this only happen for boxplot? What if you look at showMethods(exprs) or something of that nature? > > Enter a frame number, or 0 to exit > > 1: showMethods("boxplot") > 2: .showMethodsTable(getGeneric(f, where = where), includeDefs, > inherited, cla > 3: get(if (inherited) ".AllMTable" else ".MTable", envir = env) > > > > validObject(affy.batch) > Error in validObject(affy.batch) : > invalid class "AffyBatch" object: sampleNames differ between assayData > and phenoData This is a bit easier to fix. Simply change the sampleNames on one of the two structures to be the same as the others. Basically this is saying that the column names for your expression data do not agree with the row names of the phenotypic data. They might be different, or they might be out of order. You should look at both again using the AffyBatch example data: colnames(exprs(affybatch.example)) rownames(pData(affybatch.example)) need to be the same. If they are not then you need to figure out why not and fix them (maybe they are not in the same order, or one of them might be missing). I hope that helps Robert > > Enter a frame number, or 0 to exit > > 1: validObject(affy.batch) > > > par(mfrow=c(2, 1)) > > ArrayIndex = as.character(1:length(sampleNames(affy.batch))) > > > boxplot(affy.batch,names=ArrayIndex,ylab="Log2(Intensity)",xlab="Array > Index") > Error in attr(groups, "names") <- names : > 'names' attribute [80] must be the same length as the vector [1] > > Enter a frame number, or 0 to exit > > 1: boxplot(affy.batch, names = ArrayIndex, ylab = "Log2(Intensity)", > xlab = "A > 2: boxplot(affy.batch, names = ArrayIndex, ylab = "Log2(Intensity)", > xlab = "A > 3: boxplot.default(affy.batch, names = ArrayIndex, ylab = > "Log2(Intensity)", x > > Selection: > > --- > > Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry > Indiana University School of Medicine > > 15032 Hunter Court, Westfield, IN 46074 > > (317) 490-5129 Work, & Mobile & VoiceMail > (317) 663-0513 Home (no voice mail please) > > ****************************************************************** > > Robert Gentleman wrote: >> It looks to me like you are using a function named QCReport, not >> QAReport (and indeed there is no such thing - you might look at >> affyQAReport, which is in the same package but is very different). >> >> You can try to see what is happening by looking at the code from >> signalDist: >> >> par(mfrow=c(2, 1)) >> ArrayIndex = as.character(1:length(sampleNames(object))) >> boxplot(object,names=ArrayIndex,ylab="Log2(Intensity)",xlab="Array >> Index") >> >> >> where instead of object you use affy.batch.sub. The code looks pretty >> straightforward, so I don't know what the problem might be. It is a >> bit odd, it seems to me to use integers in place of the sample names... >> >> I used the affybatch.example and it worked for me.. ( one issue with >> that was >> Warning message: >> In data.row.names(row.names, rowsi, i) : >> some row.names duplicated: >> 2,26,51,76,101,126,151,176,201,226,251,276,301,326,351,376,401,426, 451,476,501,526,551,576,601,626,651,676,701,726,751,776,801,826, >> >> .... >> >> which we may need to look at). >> >> best wishes >> Robert >> >> >> Mark W Kimpel wrote: >>> I am running into an error when I run QAReport on an affybatch >>> object. Below is my sessionInfo and output. I am using the devel >>> versions of R and BioC, all newly updated. Please advise. >>> >>> Thanks, >>> Mark >>> >>> Browse[1]> sessionInfo() >>> R version 2.6.0 Under development (unstable) (2007-06-30 r42095) >>> i686-pc-linux-gnu >>> >>> locale: >>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=e n_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en _US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.U TF-8;LC_IDENTIFICATION=C >>> >>> >>> attached base packages: >>> [1] grDevices datasets splines graphics stats tools utils >>> [8] methods base >>> >>> other attached packages: >>> [1] hgu95av2cdf_1.17.0 rat2302cdf_1.17.0 affyQCReport_1.15.2 >>> [4] geneplotter_1.15.2 lattice_0.16-2 RColorBrewer_1.0-1 >>> [7] affyPLM_1.13.6 affydata_1.11.2 simpleaffy_2.11.21 >>> [10] affycoretools_1.9.2 annaffy_1.9.1 xtable_1.4-6 >>> [13] gcrma_2.9.1 matchprobes_1.9.10 biomaRt_1.11.4 >>> [16] RCurl_0.8-1 XML_1.9-0 GOstats_2.3.8 >>> [19] Category_2.3.16 genefilter_1.15.3 survival_2.32 >>> [22] KEGG_1.17.0 RBGL_1.13.3 annotate_1.15.2 >>> [25] AnnotationDbi_0.0.83 RSQLite_0.6-0 DBI_0.2-3 >>> [28] GO_1.17.0 graph_1.15.10 limma_2.11.9 >>> [31] affy_1.15.7 preprocessCore_0.99.12 affyio_1.5.6 >>> [34] Biobase_1.15.21 >>> >>> loaded via a namespace (and not attached): >>> [1] cluster_1.11.7 grid_2.6.0 KernSmooth_2.22-20 >>> >>> > affy.batch.sub >>> AffyBatch object >>> size of arrays=834x834 features (14 kb) >>> cdf=Rat230_2 (31099 affyids) >>> number of samples=16 >>> number of genes=31099 >>> annotation=rat2302 >>> notes= >>> > QCReport(affy.batch.sub) >>> Error in attr(groups, "names") <- names : >>> 'names' attribute [16] must be the same length as the vector [1] >>> >>> Enter a frame number, or 0 to exit >>> >>> 1: QCReport(affy.batch.sub) >>> 2: signalDist(object) >>> 3: boxplot(object, names = ArrayIndex, ylab = "Log2(Intensity)", xlab >>> = "Array >>> 4: boxplot.default(object, names = ArrayIndex, ylab = >>> "Log2(Intensity)", xlab >>> >>> Selection: 4 >>> Called from: eval(expr, envir, enclos) >>> Browse[1]> ls() >>> [1] "add" "args" "at" "border" "col" >>> [6] "groups" "horizontal" "log" "n" "namedargs" >>> [11] "names" "notch" "outline" "pars" "plot" >>> [16] "range" "*tmp*" "varwidth" "width" "x" >>> Browse[1]> names >>> [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" >>> "13" "14" "15" >>> [16] "16" >>> Browse[1]> names(group) >>> NULL >>> Browse[1]> names(groups) >>> [1] "" >>> Browse[1]> names(groups) <- names >>> Error during wrapup: 'names' attribute [16] must be the same length >>> as the vector [1] >>> Browse[1]> >> > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org
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I believe I have identified at least one potential contributor to the problem. In my .Rprofile, the very last like is "require(affycoretools)". I have this because affycoretools loads so many of the packages I use every day. When I start R without .Rprofile, QCReport works fine, but when I use .Rprofile, I get the following slew of error messages, which I sheepishly have to admit I have been ignoring because I wasn't having any problems. Of note is the lines: "The following object(s) are masked from package:affy : barplot," It looks to me like some of the base packages are loading after affy and this is causing problems. However, now that I have gotten QCReport to run, I am having trouble with affyQAReport. I am running R on a Linux machine with 4GB of RAM, and when I run affyQAReport on 80 rat2302 arrays I get an out of memory message. When I subset the affybatch down to 16 arrays, I get the following error "affyQAReport(affyB = affy.batch.sub, output = "pdf", outdir = "~/Genomics/TL01-05/affyQA", overwrite = FALSE, repName = "affyQAreport.pdf") Error in affyQAReport(affyB = affy.batch.sub, output = "pdf", outdir = "~/Genomics/TL01-05/affyQA", : could not find function "dist2" I agree that this is odd behavior. If you think I should reinstall R and packages, I'll do it. Below is the full output of my R startup if I have .Rprofile in play and load affycoretools on bootup. Mark R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. Loading required package: utils [1] "packages do not need updated" Loading required package: RSPerl Error in dyn.load(file, ...) : unable to load shared library '/home/mkimpel/R_HOME/R-devel/R-build/site- library/RSPerl/libs/RSPerl.so': /home/mkimpel/R_HOME/R-devel/R-build/site- library/RSPerl/libs/RSPerl.so: undefined symbol: Rf_initEmbeddedR In addition: There were 18 warnings (use warnings() to see them) sh: -c: line 0: syntax error near unexpected token `(' sh: -c: line 0: `./WriteXLS.pl --CSVpath=CSVFILES.tmp/ --CSVfiles=*.csv paste(oldwd, TestReport.xls, sep='/')' Loading required package: affycoretools Loading required package: affy Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: affyio Loading required package: preprocessCore Loading required package: limma Loading required package: GOstats Loading required package: graph Loading required package: GO Loading required package: annotate Loading required package: AnnotationDbi Loading required package: DBI Loading required package: RSQLite Loading required package: RBGL Loading required package: Category Loading required package: KEGG Loading required package: genefilter Loading required package: survival Loading required package: stats Attaching package: 'stats' The following object(s) are masked from package:affy : update Loading required package: graphics Attaching package: 'graphics' The following object(s) are masked from package:affy : barplot, boxplot, hist, image Loading required package: splines Loading required package: biomaRt Loading required package: XML Attaching package: 'XML' The following object(s) are masked from package:graph : addNode Loading required package: RCurl Attaching package: 'biomaRt' The following object(s) are masked from package:annotate : getGO Loading required package: gcrma Loading required package: matchprobes Loading required package: xtable Loading required package: annaffy Attaching package: 'affycoretools' The following object(s) are masked _by_ .GlobalEnv : vennCounts2, vennSelect > if(!exists("baseenv", mode="function")) baseenv <- function() NULL > options(STERM='iESS', editor='emacsclient') > --- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please) ****************************************************************** Robert Gentleman wrote: > Hi Mark, > > Let's see if we cannot fix some of the problems and hopefully life > will get better. > > > Mark W Kimpel wrote: >> Seth and Robert, >> >> Looks like I may have more than one problem. To clarify one point >> first, in my original post I was using affy.batch.sub, which consisted >> of just some of the arrays from my affy.batch. To make sure I'm not >> having a problem with subsetting, in my subsequent posts I am using >> the affybatch object created just today with ReadAffy. No old versions >> here, just what comes out of my sessionInfo(). >> >> As you can see below, there may be a problem with my boxplot method >> but also with the affybatch object. The latter is of class AffyBatch >> but is not a valid object. >> >> Thanks, Mark >> >> > class(affy.batch) >> [1] "AffyBatch" >> attr(,"package") >> [1] "affy" >> >> > require(affy) >> > showMethods("boxplot") >> Error in get(if (inherited) ".AllMTable" else ".MTable", envir = env) : >> variable ".AllMTable" was not found > > there is something very odd about this - I have not seen it before, > but it suggests that you might need to do a clean re-install of R and > packages as something in the methods package (I think) is very confused. > Not good news, I know, but you should not have this problem. And just to > be sure this happens if you just start up R, load the affy library and > then issue the commands above? That is what you need to check. > > > Does this only happen for boxplot? What if you look at > showMethods(exprs) or something of that nature? > >> >> Enter a frame number, or 0 to exit >> >> 1: showMethods("boxplot") >> 2: .showMethodsTable(getGeneric(f, where = where), includeDefs, >> inherited, cla >> 3: get(if (inherited) ".AllMTable" else ".MTable", envir = env) >> >> >> > validObject(affy.batch) >> Error in validObject(affy.batch) : >> invalid class "AffyBatch" object: sampleNames differ between >> assayData and phenoData > > This is a bit easier to fix. Simply change the sampleNames on one of > the two structures to be the same as the others. > > Basically this is saying that the column names for your expression > data do not agree with the row names of the phenotypic data. They might > be different, or they might be out of order. You should look at both > again using the AffyBatch example data: > > colnames(exprs(affybatch.example)) > rownames(pData(affybatch.example)) > > need to be the same. If they are not then you need to figure out why > not and fix them (maybe they are not in the same order, or one of them > might be missing). > > I hope that helps > > Robert > >> >> Enter a frame number, or 0 to exit >> >> 1: validObject(affy.batch) >> >> > par(mfrow=c(2, 1)) >> > ArrayIndex = as.character(1:length(sampleNames(affy.batch))) >> > >> boxplot(affy.batch,names=ArrayIndex,ylab="Log2(Intensity)",xlab="Array >> Index") >> Error in attr(groups, "names") <- names : >> 'names' attribute [80] must be the same length as the vector [1] >> >> Enter a frame number, or 0 to exit >> >> 1: boxplot(affy.batch, names = ArrayIndex, ylab = "Log2(Intensity)", >> xlab = "A >> 2: boxplot(affy.batch, names = ArrayIndex, ylab = "Log2(Intensity)", >> xlab = "A >> 3: boxplot.default(affy.batch, names = ArrayIndex, ylab = >> "Log2(Intensity)", x >> >> Selection: >> >> --- >> >> Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry >> Indiana University School of Medicine >> >> 15032 Hunter Court, Westfield, IN 46074 >> >> (317) 490-5129 Work, & Mobile & VoiceMail >> (317) 663-0513 Home (no voice mail please) >> >> ****************************************************************** >> >> Robert Gentleman wrote: >>> It looks to me like you are using a function named QCReport, not >>> QAReport (and indeed there is no such thing - you might look at >>> affyQAReport, which is in the same package but is very different). >>> >>> You can try to see what is happening by looking at the code from >>> signalDist: >>> >>> par(mfrow=c(2, 1)) >>> ArrayIndex = as.character(1:length(sampleNames(object))) >>> boxplot(object,names=ArrayIndex,ylab="Log2(Intensity)",xlab="Array >>> Index") >>> >>> >>> where instead of object you use affy.batch.sub. The code looks pretty >>> straightforward, so I don't know what the problem might be. It is a >>> bit odd, it seems to me to use integers in place of the sample names... >>> >>> I used the affybatch.example and it worked for me.. ( one issue with >>> that was >>> Warning message: >>> In data.row.names(row.names, rowsi, i) : >>> some row.names duplicated: >>> 2,26,51,76,101,126,151,176,201,226,251,276,301,326,351,376,401,426 ,451,476,501,526,551,576,601,626,651,676,701,726,751,776,801,826, >>> >>> .... >>> >>> which we may need to look at). >>> >>> best wishes >>> Robert >>> >>> >>> Mark W Kimpel wrote: >>>> I am running into an error when I run QAReport on an affybatch >>>> object. Below is my sessionInfo and output. I am using the devel >>>> versions of R and BioC, all newly updated. Please advise. >>>> >>>> Thanks, >>>> Mark >>>> >>>> Browse[1]> sessionInfo() >>>> R version 2.6.0 Under development (unstable) (2007-06-30 r42095) >>>> i686-pc-linux-gnu >>>> >>>> locale: >>>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE= en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=e n_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US. UTF-8;LC_IDENTIFICATION=C >>>> >>>> >>>> attached base packages: >>>> [1] grDevices datasets splines graphics stats tools utils >>>> [8] methods base >>>> >>>> other attached packages: >>>> [1] hgu95av2cdf_1.17.0 rat2302cdf_1.17.0 affyQCReport_1.15.2 >>>> [4] geneplotter_1.15.2 lattice_0.16-2 RColorBrewer_1.0-1 >>>> [7] affyPLM_1.13.6 affydata_1.11.2 simpleaffy_2.11.21 >>>> [10] affycoretools_1.9.2 annaffy_1.9.1 xtable_1.4-6 >>>> [13] gcrma_2.9.1 matchprobes_1.9.10 biomaRt_1.11.4 >>>> [16] RCurl_0.8-1 XML_1.9-0 GOstats_2.3.8 >>>> [19] Category_2.3.16 genefilter_1.15.3 survival_2.32 >>>> [22] KEGG_1.17.0 RBGL_1.13.3 annotate_1.15.2 >>>> [25] AnnotationDbi_0.0.83 RSQLite_0.6-0 DBI_0.2-3 >>>> [28] GO_1.17.0 graph_1.15.10 limma_2.11.9 >>>> [31] affy_1.15.7 preprocessCore_0.99.12 affyio_1.5.6 >>>> [34] Biobase_1.15.21 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] cluster_1.11.7 grid_2.6.0 KernSmooth_2.22-20 >>>> >>>> > affy.batch.sub >>>> AffyBatch object >>>> size of arrays=834x834 features (14 kb) >>>> cdf=Rat230_2 (31099 affyids) >>>> number of samples=16 >>>> number of genes=31099 >>>> annotation=rat2302 >>>> notes= >>>> > QCReport(affy.batch.sub) >>>> Error in attr(groups, "names") <- names : >>>> 'names' attribute [16] must be the same length as the vector [1] >>>> >>>> Enter a frame number, or 0 to exit >>>> >>>> 1: QCReport(affy.batch.sub) >>>> 2: signalDist(object) >>>> 3: boxplot(object, names = ArrayIndex, ylab = "Log2(Intensity)", >>>> xlab = "Array >>>> 4: boxplot.default(object, names = ArrayIndex, ylab = >>>> "Log2(Intensity)", xlab >>>> >>>> Selection: 4 >>>> Called from: eval(expr, envir, enclos) >>>> Browse[1]> ls() >>>> [1] "add" "args" "at" "border" "col" >>>> [6] "groups" "horizontal" "log" "n" "namedargs" >>>> [11] "names" "notch" "outline" "pars" "plot" >>>> [16] "range" "*tmp*" "varwidth" "width" "x" >>>> Browse[1]> names >>>> [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" >>>> "13" "14" "15" >>>> [16] "16" >>>> Browse[1]> names(group) >>>> NULL >>>> Browse[1]> names(groups) >>>> [1] "" >>>> Browse[1]> names(groups) <- names >>>> Error during wrapup: 'names' attribute [16] must be the same length >>>> as the vector [1] >>>> Browse[1]> >>> >> >
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Hi, Mark W Kimpel wrote: > I believe I have identified at least one potential contributor to the > problem. In my .Rprofile, the very last like is > "require(affycoretools)". I have this because affycoretools loads so > many of the packages I use every day. When I start R without .Rprofile, > QCReport works fine, but when I use .Rprofile, I get the following slew > of error messages, which I sheepishly have to admit I have been ignoring > because I wasn't having any problems. Of note is the lines: > > "The following object(s) are masked from package:affy : > > barplot," > > It looks to me like some of the base packages are loading after affy and > this is causing problems. Ignoring error/warning messages is really your call, but please do include such information with your initial post - it is kind of important for those of us trying to figure out what has gone wrong. And yes, that does seem to be a part of the problem. You can, and probably should explicitly load the base packages before any others and that should help sort out the masking. > > However, now that I have gotten QCReport to run, I am having trouble > with affyQAReport. I am running R on a Linux machine with 4GB of RAM, > and when I run affyQAReport on 80 rat2302 arrays I get an out of memory > message. When I subset the affybatch down to 16 arrays, I get the > following error Tracking down the memory issue will be harder - basically there are some inefficiencies, but I am not just sure where they might be. If you could run this with options(error=recover) and give some info on where in the computations it is happening that would help - but a quicker fix is going to be more RAM, I think. > > "affyQAReport(affyB = affy.batch.sub, output = "pdf", outdir = > "~/Genomics/TL01-05/affyQA", overwrite = FALSE, repName = > "affyQAreport.pdf") > > Error in affyQAReport(affyB = affy.batch.sub, output = "pdf", outdir = > "~/Genomics/TL01-05/affyQA", : > could not find function "dist2" This was what I had expected - a bug in genefilter that I finally tracked down on Friday - I think that if you do an update.packages now you will see that you get a new version, and that this error message will go away. > > I agree that this is odd behavior. If you think I should reinstall R and > packages, I'll do it. Below is the full output of my R startup if I have > .Rprofile in play and load affycoretools on bootup. no things should be a bit better now > > Mark > > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > > Loading required package: utils > [1] "packages do not need updated" > Loading required package: RSPerl > Error in dyn.load(file, ...) : > unable to load shared library > '/home/mkimpel/R_HOME/R-devel/R-build/site- library/RSPerl/libs/RSPerl.so': > > /home/mkimpel/R_HOME/R-devel/R-build/site- library/RSPerl/libs/RSPerl.so: > undefined symbol: Rf_initEmbeddedR > In addition: There were 18 warnings (use warnings() to see them) > sh: -c: line 0: syntax error near unexpected token `(' > sh: -c: line 0: `./WriteXLS.pl --CSVpath=CSVFILES.tmp/ --CSVfiles=*.csv This is worth reporting to the maintainer of RSPerl > paste(oldwd, TestReport.xls, sep='/')' > Loading required package: affycoretools > Loading required package: affy > Loading required package: Biobase > Loading required package: tools > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > Loading required package: affyio > Loading required package: preprocessCore > Loading required package: limma > Loading required package: GOstats > Loading required package: graph > Loading required package: GO > Loading required package: annotate > Loading required package: AnnotationDbi > Loading required package: DBI > Loading required package: RSQLite > Loading required package: RBGL > Loading required package: Category > Loading required package: KEGG > Loading required package: genefilter > Loading required package: survival > Loading required package: stats > > Attaching package: 'stats' > > > The following object(s) are masked from package:affy : > > update > > Loading required package: graphics > > Attaching package: 'graphics' > > > The following object(s) are masked from package:affy : > > barplot, > boxplot, > hist, > image > > Loading required package: splines > Loading required package: biomaRt > Loading required package: XML > > Attaching package: 'XML' > > > The following object(s) are masked from package:graph : > > addNode > > Loading required package: RCurl > > Attaching package: 'biomaRt' > > > The following object(s) are masked from package:annotate : > > getGO > > Loading required package: gcrma > Loading required package: matchprobes > Loading required package: xtable > Loading required package: annaffy > > Attaching package: 'affycoretools' > > > The following object(s) are masked _by_ .GlobalEnv : > > vennCounts2, > vennSelect > > > if(!exists("baseenv", mode="function")) baseenv <- function() NULL > > options(STERM='iESS', editor='emacsclient') > > > > --- > > Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry > Indiana University School of Medicine > > 15032 Hunter Court, Westfield, IN 46074 > > (317) 490-5129 Work, & Mobile & VoiceMail > (317) 663-0513 Home (no voice mail please) > > ****************************************************************** > > Robert Gentleman wrote: >> Hi Mark, >> >> Let's see if we cannot fix some of the problems and hopefully life >> will get better. >> >> >> Mark W Kimpel wrote: >>> Seth and Robert, >>> >>> Looks like I may have more than one problem. To clarify one point >>> first, in my original post I was using affy.batch.sub, which >>> consisted of just some of the arrays from my affy.batch. To make sure >>> I'm not having a problem with subsetting, in my subsequent posts I am >>> using the affybatch object created just today with ReadAffy. No old >>> versions here, just what comes out of my sessionInfo(). >>> >>> As you can see below, there may be a problem with my boxplot method >>> but also with the affybatch object. The latter is of class AffyBatch >>> but is not a valid object. >>> >>> Thanks, Mark >>> >>> > class(affy.batch) >>> [1] "AffyBatch" >>> attr(,"package") >>> [1] "affy" >>> >>> > require(affy) >>> > showMethods("boxplot") >>> Error in get(if (inherited) ".AllMTable" else ".MTable", envir = env) : >>> variable ".AllMTable" was not found >> >> there is something very odd about this - I have not seen it before, >> but it suggests that you might need to do a clean re-install of R and >> packages as something in the methods package (I think) is very confused. >> Not good news, I know, but you should not have this problem. And just >> to be sure this happens if you just start up R, load the affy library >> and then issue the commands above? That is what you need to check. >> >> >> Does this only happen for boxplot? What if you look at >> showMethods(exprs) or something of that nature? >> >>> >>> Enter a frame number, or 0 to exit >>> >>> 1: showMethods("boxplot") >>> 2: .showMethodsTable(getGeneric(f, where = where), includeDefs, >>> inherited, cla >>> 3: get(if (inherited) ".AllMTable" else ".MTable", envir = env) >>> >>> >>> > validObject(affy.batch) >>> Error in validObject(affy.batch) : >>> invalid class "AffyBatch" object: sampleNames differ between >>> assayData and phenoData >> >> This is a bit easier to fix. Simply change the sampleNames on one of >> the two structures to be the same as the others. >> >> Basically this is saying that the column names for your expression >> data do not agree with the row names of the phenotypic data. They >> might be different, or they might be out of order. You should look at >> both >> again using the AffyBatch example data: >> >> colnames(exprs(affybatch.example)) >> rownames(pData(affybatch.example)) >> >> need to be the same. If they are not then you need to figure out why >> not and fix them (maybe they are not in the same order, or one of them >> might be missing). >> >> I hope that helps >> >> Robert >> >>> >>> Enter a frame number, or 0 to exit >>> >>> 1: validObject(affy.batch) >>> >>> > par(mfrow=c(2, 1)) >>> > ArrayIndex = as.character(1:length(sampleNames(affy.batch))) >>> > >>> boxplot(affy.batch,names=ArrayIndex,ylab="Log2(Intensity)",xlab="Array >>> Index") >>> Error in attr(groups, "names") <- names : >>> 'names' attribute [80] must be the same length as the vector [1] >>> >>> Enter a frame number, or 0 to exit >>> >>> 1: boxplot(affy.batch, names = ArrayIndex, ylab = "Log2(Intensity)", >>> xlab = "A >>> 2: boxplot(affy.batch, names = ArrayIndex, ylab = "Log2(Intensity)", >>> xlab = "A >>> 3: boxplot.default(affy.batch, names = ArrayIndex, ylab = >>> "Log2(Intensity)", x >>> >>> Selection: >>> >>> --- >>> >>> Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry >>> Indiana University School of Medicine >>> >>> 15032 Hunter Court, Westfield, IN 46074 >>> >>> (317) 490-5129 Work, & Mobile & VoiceMail >>> (317) 663-0513 Home (no voice mail please) >>> >>> ****************************************************************** >>> >>> Robert Gentleman wrote: >>>> It looks to me like you are using a function named QCReport, not >>>> QAReport (and indeed there is no such thing - you might look at >>>> affyQAReport, which is in the same package but is very different). >>>> >>>> You can try to see what is happening by looking at the code from >>>> signalDist: >>>> >>>> par(mfrow=c(2, 1)) >>>> ArrayIndex = as.character(1:length(sampleNames(object))) >>>> boxplot(object,names=ArrayIndex,ylab="Log2(Intensity)",xlab="Array >>>> Index") >>>> >>>> >>>> where instead of object you use affy.batch.sub. The code looks >>>> pretty straightforward, so I don't know what the problem might be. >>>> It is a bit odd, it seems to me to use integers in place of the >>>> sample names... >>>> >>>> I used the affybatch.example and it worked for me.. ( one issue with >>>> that was >>>> Warning message: >>>> In data.row.names(row.names, rowsi, i) : >>>> some row.names duplicated: >>>> 2,26,51,76,101,126,151,176,201,226,251,276,301,326,351,376,401,42 6,451,476,501,526,551,576,601,626,651,676,701,726,751,776,801,826, >>>> >>>> .... >>>> >>>> which we may need to look at). >>>> >>>> best wishes >>>> Robert >>>> >>>> >>>> Mark W Kimpel wrote: >>>>> I am running into an error when I run QAReport on an affybatch >>>>> object. Below is my sessionInfo and output. I am using the devel >>>>> versions of R and BioC, all newly updated. Please advise. >>>>> >>>>> Thanks, >>>>> Mark >>>>> >>>>> Browse[1]> sessionInfo() >>>>> R version 2.6.0 Under development (unstable) (2007-06-30 r42095) >>>>> i686-pc-linux-gnu >>>>> >>>>> locale: >>>>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE =en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER= en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US .UTF-8;LC_IDENTIFICATION=C >>>>> >>>>> >>>>> attached base packages: >>>>> [1] grDevices datasets splines graphics stats tools utils >>>>> [8] methods base >>>>> >>>>> other attached packages: >>>>> [1] hgu95av2cdf_1.17.0 rat2302cdf_1.17.0 >>>>> affyQCReport_1.15.2 >>>>> [4] geneplotter_1.15.2 lattice_0.16-2 RColorBrewer_1.0-1 >>>>> [7] affyPLM_1.13.6 affydata_1.11.2 simpleaffy_2.11.21 >>>>> [10] affycoretools_1.9.2 annaffy_1.9.1 xtable_1.4-6 >>>>> [13] gcrma_2.9.1 matchprobes_1.9.10 biomaRt_1.11.4 >>>>> [16] RCurl_0.8-1 XML_1.9-0 GOstats_2.3.8 >>>>> [19] Category_2.3.16 genefilter_1.15.3 survival_2.32 >>>>> [22] KEGG_1.17.0 RBGL_1.13.3 annotate_1.15.2 >>>>> [25] AnnotationDbi_0.0.83 RSQLite_0.6-0 DBI_0.2-3 >>>>> [28] GO_1.17.0 graph_1.15.10 limma_2.11.9 >>>>> [31] affy_1.15.7 preprocessCore_0.99.12 affyio_1.5.6 >>>>> [34] Biobase_1.15.21 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] cluster_1.11.7 grid_2.6.0 KernSmooth_2.22-20 >>>>> >>>>> > affy.batch.sub >>>>> AffyBatch object >>>>> size of arrays=834x834 features (14 kb) >>>>> cdf=Rat230_2 (31099 affyids) >>>>> number of samples=16 >>>>> number of genes=31099 >>>>> annotation=rat2302 >>>>> notes= >>>>> > QCReport(affy.batch.sub) >>>>> Error in attr(groups, "names") <- names : >>>>> 'names' attribute [16] must be the same length as the vector [1] >>>>> >>>>> Enter a frame number, or 0 to exit >>>>> >>>>> 1: QCReport(affy.batch.sub) >>>>> 2: signalDist(object) >>>>> 3: boxplot(object, names = ArrayIndex, ylab = "Log2(Intensity)", >>>>> xlab = "Array >>>>> 4: boxplot.default(object, names = ArrayIndex, ylab = >>>>> "Log2(Intensity)", xlab >>>>> >>>>> Selection: 4 >>>>> Called from: eval(expr, envir, enclos) >>>>> Browse[1]> ls() >>>>> [1] "add" "args" "at" "border" "col" >>>>> [6] "groups" "horizontal" "log" "n" "namedargs" >>>>> [11] "names" "notch" "outline" "pars" "plot" >>>>> [16] "range" "*tmp*" "varwidth" "width" "x" >>>>> Browse[1]> names >>>>> [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" >>>>> "13" "14" "15" >>>>> [16] "16" >>>>> Browse[1]> names(group) >>>>> NULL >>>>> Browse[1]> names(groups) >>>>> [1] "" >>>>> Browse[1]> names(groups) <- names >>>>> Error during wrapup: 'names' attribute [16] must be the same length >>>>> as the vector [1] >>>>> Browse[1]> >>>> >>> >> > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org
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It looks to me like you are using a function named QCReport, not QAReport (and indeed there is no such thing - you might look at affyQAReport, which is in the same package but is very different). You can try to see what is happening by looking at the code from signalDist: par(mfrow=c(2, 1)) ArrayIndex = as.character(1:length(sampleNames(object))) boxplot(object,names=ArrayIndex,ylab="Log2(Intensity)",xlab="Array Index") where instead of object you use affy.batch.sub. The code looks pretty straightforward, so I don't know what the problem might be. It is a bit odd, it seems to me to use integers in place of the sample names... I used the affybatch.example and it worked for me.. ( one issue with that was Warning message: In data.row.names(row.names, rowsi, i) : some row.names duplicated: 2,26,51,76,101,126,151,176,201,226,251,276,301,326,351,376,401,426,451 ,476,501,526,551,576,601,626,651,676,701,726,751,776,801,826, .... which we may need to look at). best wishes Robert Mark W Kimpel wrote: > I am running into an error when I run QAReport on an affybatch object. > Below is my sessionInfo and output. I am using the devel versions of R > and BioC, all newly updated. Please advise. > > Thanks, > Mark > > Browse[1]> sessionInfo() > R version 2.6.0 Under development (unstable) (2007-06-30 r42095) > i686-pc-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_U S.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF -8;LC_IDENTIFICATION=C > > attached base packages: > [1] grDevices datasets splines graphics stats tools utils > [8] methods base > > other attached packages: > [1] hgu95av2cdf_1.17.0 rat2302cdf_1.17.0 affyQCReport_1.15.2 > [4] geneplotter_1.15.2 lattice_0.16-2 RColorBrewer_1.0-1 > [7] affyPLM_1.13.6 affydata_1.11.2 simpleaffy_2.11.21 > [10] affycoretools_1.9.2 annaffy_1.9.1 xtable_1.4-6 > [13] gcrma_2.9.1 matchprobes_1.9.10 biomaRt_1.11.4 > [16] RCurl_0.8-1 XML_1.9-0 GOstats_2.3.8 > [19] Category_2.3.16 genefilter_1.15.3 survival_2.32 > [22] KEGG_1.17.0 RBGL_1.13.3 annotate_1.15.2 > [25] AnnotationDbi_0.0.83 RSQLite_0.6-0 DBI_0.2-3 > [28] GO_1.17.0 graph_1.15.10 limma_2.11.9 > [31] affy_1.15.7 preprocessCore_0.99.12 affyio_1.5.6 > [34] Biobase_1.15.21 > > loaded via a namespace (and not attached): > [1] cluster_1.11.7 grid_2.6.0 KernSmooth_2.22-20 > > > affy.batch.sub > AffyBatch object > size of arrays=834x834 features (14 kb) > cdf=Rat230_2 (31099 affyids) > number of samples=16 > number of genes=31099 > annotation=rat2302 > notes= > > QCReport(affy.batch.sub) > Error in attr(groups, "names") <- names : > 'names' attribute [16] must be the same length as the vector [1] > > Enter a frame number, or 0 to exit > > 1: QCReport(affy.batch.sub) > 2: signalDist(object) > 3: boxplot(object, names = ArrayIndex, ylab = "Log2(Intensity)", xlab = > "Array > 4: boxplot.default(object, names = ArrayIndex, ylab = "Log2(Intensity)", > xlab > > Selection: 4 > Called from: eval(expr, envir, enclos) > Browse[1]> ls() > [1] "add" "args" "at" "border" "col" > [6] "groups" "horizontal" "log" "n" "namedargs" > [11] "names" "notch" "outline" "pars" "plot" > [16] "range" "*tmp*" "varwidth" "width" "x" > Browse[1]> names > [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" > "14" "15" > [16] "16" > Browse[1]> names(group) > NULL > Browse[1]> names(groups) > [1] "" > Browse[1]> names(groups) <- names > Error during wrapup: 'names' attribute [16] must be the same length as > the vector [1] > Browse[1]> -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org
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Robert, You are correct, I am using the function QCReport. I downloaded the source code of the packages affy and affyQCReport and believe the problem may be that the wrong method is being called when boxplot is invoked on my affybatch object. I get an error when I do signature(affy.batch). See below... Is this expected behavior? Could my affybatch object be corrupted? Mark > signature(affy.batch) Error in signature(affy.batch) : bad class specified for element 1 (should be a single character string) Enter a frame number, or 0 to exit 1: signature(affy.batch) Selection: 1 Called from: eval(expr, envir, enclos) Browse[1]> ls() [1] "i" "names" "sigi" "value" Browse[1]> value [[1]] AffyBatch object size of arrays=834x834 features (23 kb) cdf=Rat230_2 (31099 affyids) number of samples=80 number of genes=31099 annotation=rat2302 notes= Browse[1]> i [1] 1 Browse[1]> names NULL Browse[1]> sigi AffyBatch object size of arrays=834x834 features (23 kb) cdf=Rat230_2 (31099 affyids) number of samples=80 number of genes=31099 annotation=rat2302 notes= Browse[1]> Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please) ****************************************************************** Robert Gentleman wrote: > It looks to me like you are using a function named QCReport, not > QAReport (and indeed there is no such thing - you might look at > affyQAReport, which is in the same package but is very different). > > You can try to see what is happening by looking at the code from > signalDist: > > par(mfrow=c(2, 1)) > ArrayIndex = as.character(1:length(sampleNames(object))) > boxplot(object,names=ArrayIndex,ylab="Log2(Intensity)",xlab="Array Index") > > > where instead of object you use affy.batch.sub. The code looks pretty > straightforward, so I don't know what the problem might be. It is a bit > odd, it seems to me to use integers in place of the sample names... > > I used the affybatch.example and it worked for me.. ( one issue with > that was > Warning message: > In data.row.names(row.names, rowsi, i) : > some row.names duplicated: > 2,26,51,76,101,126,151,176,201,226,251,276,301,326,351,376,401,426,4 51,476,501,526,551,576,601,626,651,676,701,726,751,776,801,826, > > .... > > which we may need to look at). > > best wishes > Robert > > > Mark W Kimpel wrote: >> I am running into an error when I run QAReport on an affybatch object. >> Below is my sessionInfo and output. I am using the devel versions of R >> and BioC, all newly updated. Please advise. >> >> Thanks, >> Mark >> >> Browse[1]> sessionInfo() >> R version 2.6.0 Under development (unstable) (2007-06-30 r42095) >> i686-pc-linux-gnu >> >> locale: >> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en _US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_ US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UT F-8;LC_IDENTIFICATION=C >> >> >> attached base packages: >> [1] grDevices datasets splines graphics stats tools utils >> [8] methods base >> >> other attached packages: >> [1] hgu95av2cdf_1.17.0 rat2302cdf_1.17.0 affyQCReport_1.15.2 >> [4] geneplotter_1.15.2 lattice_0.16-2 RColorBrewer_1.0-1 >> [7] affyPLM_1.13.6 affydata_1.11.2 simpleaffy_2.11.21 >> [10] affycoretools_1.9.2 annaffy_1.9.1 xtable_1.4-6 >> [13] gcrma_2.9.1 matchprobes_1.9.10 biomaRt_1.11.4 >> [16] RCurl_0.8-1 XML_1.9-0 GOstats_2.3.8 >> [19] Category_2.3.16 genefilter_1.15.3 survival_2.32 >> [22] KEGG_1.17.0 RBGL_1.13.3 annotate_1.15.2 >> [25] AnnotationDbi_0.0.83 RSQLite_0.6-0 DBI_0.2-3 >> [28] GO_1.17.0 graph_1.15.10 limma_2.11.9 >> [31] affy_1.15.7 preprocessCore_0.99.12 affyio_1.5.6 >> [34] Biobase_1.15.21 >> >> loaded via a namespace (and not attached): >> [1] cluster_1.11.7 grid_2.6.0 KernSmooth_2.22-20 >> >> > affy.batch.sub >> AffyBatch object >> size of arrays=834x834 features (14 kb) >> cdf=Rat230_2 (31099 affyids) >> number of samples=16 >> number of genes=31099 >> annotation=rat2302 >> notes= >> > QCReport(affy.batch.sub) >> Error in attr(groups, "names") <- names : >> 'names' attribute [16] must be the same length as the vector [1] >> >> Enter a frame number, or 0 to exit >> >> 1: QCReport(affy.batch.sub) >> 2: signalDist(object) >> 3: boxplot(object, names = ArrayIndex, ylab = "Log2(Intensity)", xlab >> = "Array >> 4: boxplot.default(object, names = ArrayIndex, ylab = >> "Log2(Intensity)", xlab >> >> Selection: 4 >> Called from: eval(expr, envir, enclos) >> Browse[1]> ls() >> [1] "add" "args" "at" "border" "col" >> [6] "groups" "horizontal" "log" "n" "namedargs" >> [11] "names" "notch" "outline" "pars" "plot" >> [16] "range" "*tmp*" "varwidth" "width" "x" >> Browse[1]> names >> [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" >> "14" "15" >> [16] "16" >> Browse[1]> names(group) >> NULL >> Browse[1]> names(groups) >> [1] "" >> Browse[1]> names(groups) <- names >> Error during wrapup: 'names' attribute [16] must be the same length as >> the vector [1] >> Browse[1]> >
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Mark W Kimpel wrote: > Robert, > > You are correct, I am using the function QCReport. I downloaded the > source code of the packages affy and affyQCReport and believe the > problem may be that the wrong method is being called when boxplot is > invoked on my affybatch object. I get an error when I do > signature(affy.batch). See below... Is this expected behavior? Could my > affybatch object be corrupted? Mark It could well be, but that is not what signature is for. You want class(affy.batch) - but you were using a subset of that I thought. It is possible to get both corrupted objects (especially if they are old and may have been created with a previous version of R) and also method dispatch can get confused. I cannot tell from what you have sent which is like to be your problem. Please check the class of the object, and also run the code I sent in the previous email with all output, that might help to figure out just what your problem is. It might also help to see the output of search and potentially of showMethods. I get: > showMethods("boxplot") Function: boxplot (package graphics) x="ANY" x="AffyBatch" with the affy package attached. best wishes Robert > > > signature(affy.batch) > Error in signature(affy.batch) : > bad class specified for element 1 (should be a single character string) > > Enter a frame number, or 0 to exit > > 1: signature(affy.batch) > > Selection: 1 > Called from: eval(expr, envir, enclos) > Browse[1]> ls() > [1] "i" "names" "sigi" "value" > Browse[1]> value > [[1]] > AffyBatch object > size of arrays=834x834 features (23 kb) > cdf=Rat230_2 (31099 affyids) > number of samples=80 > number of genes=31099 > annotation=rat2302 > notes= > > Browse[1]> i > [1] 1 > Browse[1]> names > NULL > Browse[1]> sigi > AffyBatch object > size of arrays=834x834 features (23 kb) > cdf=Rat230_2 (31099 affyids) > number of samples=80 > number of genes=31099 > annotation=rat2302 > notes= > Browse[1]> > > Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry > Indiana University School of Medicine > > 15032 Hunter Court, Westfield, IN 46074 > > (317) 490-5129 Work, & Mobile & VoiceMail > (317) 663-0513 Home (no voice mail please) > > ****************************************************************** > > Robert Gentleman wrote: >> It looks to me like you are using a function named QCReport, not >> QAReport (and indeed there is no such thing - you might look at >> affyQAReport, which is in the same package but is very different). >> >> You can try to see what is happening by looking at the code from >> signalDist: >> >> par(mfrow=c(2, 1)) >> ArrayIndex = as.character(1:length(sampleNames(object))) >> boxplot(object,names=ArrayIndex,ylab="Log2(Intensity)",xlab="Array >> Index") >> >> >> where instead of object you use affy.batch.sub. The code looks pretty >> straightforward, so I don't know what the problem might be. It is a >> bit odd, it seems to me to use integers in place of the sample names... >> >> I used the affybatch.example and it worked for me.. ( one issue with >> that was >> Warning message: >> In data.row.names(row.names, rowsi, i) : >> some row.names duplicated: >> 2,26,51,76,101,126,151,176,201,226,251,276,301,326,351,376,401,426, 451,476,501,526,551,576,601,626,651,676,701,726,751,776,801,826, >> >> .... >> >> which we may need to look at). >> >> best wishes >> Robert >> >> >> Mark W Kimpel wrote: >>> I am running into an error when I run QAReport on an affybatch >>> object. Below is my sessionInfo and output. I am using the devel >>> versions of R and BioC, all newly updated. Please advise. >>> >>> Thanks, >>> Mark >>> >>> Browse[1]> sessionInfo() >>> R version 2.6.0 Under development (unstable) (2007-06-30 r42095) >>> i686-pc-linux-gnu >>> >>> locale: >>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=e n_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en _US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.U TF-8;LC_IDENTIFICATION=C >>> >>> >>> attached base packages: >>> [1] grDevices datasets splines graphics stats tools utils >>> [8] methods base >>> >>> other attached packages: >>> [1] hgu95av2cdf_1.17.0 rat2302cdf_1.17.0 affyQCReport_1.15.2 >>> [4] geneplotter_1.15.2 lattice_0.16-2 RColorBrewer_1.0-1 >>> [7] affyPLM_1.13.6 affydata_1.11.2 simpleaffy_2.11.21 >>> [10] affycoretools_1.9.2 annaffy_1.9.1 xtable_1.4-6 >>> [13] gcrma_2.9.1 matchprobes_1.9.10 biomaRt_1.11.4 >>> [16] RCurl_0.8-1 XML_1.9-0 GOstats_2.3.8 >>> [19] Category_2.3.16 genefilter_1.15.3 survival_2.32 >>> [22] KEGG_1.17.0 RBGL_1.13.3 annotate_1.15.2 >>> [25] AnnotationDbi_0.0.83 RSQLite_0.6-0 DBI_0.2-3 >>> [28] GO_1.17.0 graph_1.15.10 limma_2.11.9 >>> [31] affy_1.15.7 preprocessCore_0.99.12 affyio_1.5.6 >>> [34] Biobase_1.15.21 >>> >>> loaded via a namespace (and not attached): >>> [1] cluster_1.11.7 grid_2.6.0 KernSmooth_2.22-20 >>> >>> > affy.batch.sub >>> AffyBatch object >>> size of arrays=834x834 features (14 kb) >>> cdf=Rat230_2 (31099 affyids) >>> number of samples=16 >>> number of genes=31099 >>> annotation=rat2302 >>> notes= >>> > QCReport(affy.batch.sub) >>> Error in attr(groups, "names") <- names : >>> 'names' attribute [16] must be the same length as the vector [1] >>> >>> Enter a frame number, or 0 to exit >>> >>> 1: QCReport(affy.batch.sub) >>> 2: signalDist(object) >>> 3: boxplot(object, names = ArrayIndex, ylab = "Log2(Intensity)", xlab >>> = "Array >>> 4: boxplot.default(object, names = ArrayIndex, ylab = >>> "Log2(Intensity)", xlab >>> >>> Selection: 4 >>> Called from: eval(expr, envir, enclos) >>> Browse[1]> ls() >>> [1] "add" "args" "at" "border" "col" >>> [6] "groups" "horizontal" "log" "n" "namedargs" >>> [11] "names" "notch" "outline" "pars" "plot" >>> [16] "range" "*tmp*" "varwidth" "width" "x" >>> Browse[1]> names >>> [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" >>> "13" "14" "15" >>> [16] "16" >>> Browse[1]> names(group) >>> NULL >>> Browse[1]> names(groups) >>> [1] "" >>> Browse[1]> names(groups) <- names >>> Error during wrapup: 'names' attribute [16] must be the same length >>> as the vector [1] >>> Browse[1]> >> > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org
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Mark W Kimpel wrote: > Robert, > > You are correct, I am using the function QCReport. I downloaded the > source code of the packages affy and affyQCReport and believe the > problem may be that the wrong method is being called when boxplot is > invoked on my affybatch object. I get an error when I do > signature(affy.batch). See below... Is this expected behavior? Could my > affybatch object be corrupted? Mark It could well be, but that is not what signature is for. You want class(affy.batch) - but you were using a subset of that I thought. It is possible to get both corrupted objects (especially if they are old and may have been created with a previous version of R) and also method dispatch can get confused. I cannot tell from what you have sent which is like to be your problem. Please check the class of the object, and also run the code I sent in the previous email with all output, that might help to figure out just what your problem is. It might also help to see the output of search and potentially of showMethods. I get: > showMethods("boxplot") Function: boxplot (package graphics) x="ANY" x="AffyBatch" with the affy package attached. best wishes Robert > > > signature(affy.batch) > Error in signature(affy.batch) : > bad class specified for element 1 (should be a single character string) > > Enter a frame number, or 0 to exit > > 1: signature(affy.batch) > > Selection: 1 > Called from: eval(expr, envir, enclos) > Browse[1]> ls() > [1] "i" "names" "sigi" "value" > Browse[1]> value > [[1]] > AffyBatch object > size of arrays=834x834 features (23 kb) > cdf=Rat230_2 (31099 affyids) > number of samples=80 > number of genes=31099 > annotation=rat2302 > notes= > > Browse[1]> i > [1] 1 > Browse[1]> names > NULL > Browse[1]> sigi > AffyBatch object > size of arrays=834x834 features (23 kb) > cdf=Rat230_2 (31099 affyids) > number of samples=80 > number of genes=31099 > annotation=rat2302 > notes= > Browse[1]> > > Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry > Indiana University School of Medicine > > 15032 Hunter Court, Westfield, IN 46074 > > (317) 490-5129 Work, & Mobile & VoiceMail > (317) 663-0513 Home (no voice mail please) > > ****************************************************************** > > Robert Gentleman wrote: >> It looks to me like you are using a function named QCReport, not >> QAReport (and indeed there is no such thing - you might look at >> affyQAReport, which is in the same package but is very different). >> >> You can try to see what is happening by looking at the code from >> signalDist: >> >> par(mfrow=c(2, 1)) >> ArrayIndex = as.character(1:length(sampleNames(object))) >> boxplot(object,names=ArrayIndex,ylab="Log2(Intensity)",xlab="Array >> Index") >> >> >> where instead of object you use affy.batch.sub. The code looks pretty >> straightforward, so I don't know what the problem might be. It is a >> bit odd, it seems to me to use integers in place of the sample names... >> >> I used the affybatch.example and it worked for me.. ( one issue with >> that was >> Warning message: >> In data.row.names(row.names, rowsi, i) : >> some row.names duplicated: >> 2,26,51,76,101,126,151,176,201,226,251,276,301,326,351,376,401,426, 451,476,501,526,551,576,601,626,651,676,701,726,751,776,801,826, >> >> .... >> >> which we may need to look at). >> >> best wishes >> Robert >> >> >> Mark W Kimpel wrote: >>> I am running into an error when I run QAReport on an affybatch >>> object. Below is my sessionInfo and output. I am using the devel >>> versions of R and BioC, all newly updated. Please advise. >>> >>> Thanks, >>> Mark >>> >>> Browse[1]> sessionInfo() >>> R version 2.6.0 Under development (unstable) (2007-06-30 r42095) >>> i686-pc-linux-gnu >>> >>> locale: >>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=e n_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en _US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.U TF-8;LC_IDENTIFICATION=C >>> >>> >>> attached base packages: >>> [1] grDevices datasets splines graphics stats tools utils >>> [8] methods base >>> >>> other attached packages: >>> [1] hgu95av2cdf_1.17.0 rat2302cdf_1.17.0 affyQCReport_1.15.2 >>> [4] geneplotter_1.15.2 lattice_0.16-2 RColorBrewer_1.0-1 >>> [7] affyPLM_1.13.6 affydata_1.11.2 simpleaffy_2.11.21 >>> [10] affycoretools_1.9.2 annaffy_1.9.1 xtable_1.4-6 >>> [13] gcrma_2.9.1 matchprobes_1.9.10 biomaRt_1.11.4 >>> [16] RCurl_0.8-1 XML_1.9-0 GOstats_2.3.8 >>> [19] Category_2.3.16 genefilter_1.15.3 survival_2.32 >>> [22] KEGG_1.17.0 RBGL_1.13.3 annotate_1.15.2 >>> [25] AnnotationDbi_0.0.83 RSQLite_0.6-0 DBI_0.2-3 >>> [28] GO_1.17.0 graph_1.15.10 limma_2.11.9 >>> [31] affy_1.15.7 preprocessCore_0.99.12 affyio_1.5.6 >>> [34] Biobase_1.15.21 >>> >>> loaded via a namespace (and not attached): >>> [1] cluster_1.11.7 grid_2.6.0 KernSmooth_2.22-20 >>> >>> > affy.batch.sub >>> AffyBatch object >>> size of arrays=834x834 features (14 kb) >>> cdf=Rat230_2 (31099 affyids) >>> number of samples=16 >>> number of genes=31099 >>> annotation=rat2302 >>> notes= >>> > QCReport(affy.batch.sub) >>> Error in attr(groups, "names") <- names : >>> 'names' attribute [16] must be the same length as the vector [1] >>> >>> Enter a frame number, or 0 to exit >>> >>> 1: QCReport(affy.batch.sub) >>> 2: signalDist(object) >>> 3: boxplot(object, names = ArrayIndex, ylab = "Log2(Intensity)", xlab >>> = "Array >>> 4: boxplot.default(object, names = ArrayIndex, ylab = >>> "Log2(Intensity)", xlab >>> >>> Selection: 4 >>> Called from: eval(expr, envir, enclos) >>> Browse[1]> ls() >>> [1] "add" "args" "at" "border" "col" >>> [6] "groups" "horizontal" "log" "n" "namedargs" >>> [11] "names" "notch" "outline" "pars" "plot" >>> [16] "range" "*tmp*" "varwidth" "width" "x" >>> Browse[1]> names >>> [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" >>> "13" "14" "15" >>> [16] "16" >>> Browse[1]> names(group) >>> NULL >>> Browse[1]> names(groups) >>> [1] "" >>> Browse[1]> names(groups) <- names >>> Error during wrapup: 'names' attribute [16] must be the same length >>> as the vector [1] >>> Browse[1]> >> > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org
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Seth and Robert, Looks like I may have more than one problem. To clarify one point first, in my original post I was using affy.batch.sub, which consisted of just some of the arrays from my affy.batch. To make sure I'm not having a problem with subsetting, in my subsequent posts I am using the affybatch object created just today with ReadAffy. No old versions here, just what comes out of my sessionInfo(). As you can see below, there may be a problem with my boxplot method but also with the affybatch object. The latter is of class AffyBatch but is not a valid object. Thanks, Mark > class(affy.batch) [1] "AffyBatch" attr(,"package") [1] "affy" > require(affy) > showMethods("boxplot") Error in get(if (inherited) ".AllMTable" else ".MTable", envir = env) : variable ".AllMTable" was not found Enter a frame number, or 0 to exit 1: showMethods("boxplot") 2: .showMethodsTable(getGeneric(f, where = where), includeDefs, inherited, cla 3: get(if (inherited) ".AllMTable" else ".MTable", envir = env) > validObject(affy.batch) Error in validObject(affy.batch) : invalid class "AffyBatch" object: sampleNames differ between assayData and phenoData Enter a frame number, or 0 to exit 1: validObject(affy.batch) > par(mfrow=c(2, 1)) > ArrayIndex = as.character(1:length(sampleNames(affy.batch))) > boxplot(affy.batch,names=ArrayIndex,ylab="Log2(Intensity)",xlab="Array Index") Error in attr(groups, "names") <- names : 'names' attribute [80] must be the same length as the vector [1] Enter a frame number, or 0 to exit 1: boxplot(affy.batch, names = ArrayIndex, ylab = "Log2(Intensity)", xlab = "A 2: boxplot(affy.batch, names = ArrayIndex, ylab = "Log2(Intensity)", xlab = "A 3: boxplot.default(affy.batch, names = ArrayIndex, ylab = "Log2(Intensity)", x Selection: --- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please) ****************************************************************** Robert Gentleman wrote: > It looks to me like you are using a function named QCReport, not > QAReport (and indeed there is no such thing - you might look at > affyQAReport, which is in the same package but is very different). > > You can try to see what is happening by looking at the code from > signalDist: > > par(mfrow=c(2, 1)) > ArrayIndex = as.character(1:length(sampleNames(object))) > boxplot(object,names=ArrayIndex,ylab="Log2(Intensity)",xlab="Array Index") > > > where instead of object you use affy.batch.sub. The code looks pretty > straightforward, so I don't know what the problem might be. It is a bit > odd, it seems to me to use integers in place of the sample names... > > I used the affybatch.example and it worked for me.. ( one issue with > that was > Warning message: > In data.row.names(row.names, rowsi, i) : > some row.names duplicated: > 2,26,51,76,101,126,151,176,201,226,251,276,301,326,351,376,401,426,4 51,476,501,526,551,576,601,626,651,676,701,726,751,776,801,826, > > .... > > which we may need to look at). > > best wishes > Robert > > > Mark W Kimpel wrote: >> I am running into an error when I run QAReport on an affybatch object. >> Below is my sessionInfo and output. I am using the devel versions of R >> and BioC, all newly updated. Please advise. >> >> Thanks, >> Mark >> >> Browse[1]> sessionInfo() >> R version 2.6.0 Under development (unstable) (2007-06-30 r42095) >> i686-pc-linux-gnu >> >> locale: >> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en _US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_ US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UT F-8;LC_IDENTIFICATION=C >> >> >> attached base packages: >> [1] grDevices datasets splines graphics stats tools utils >> [8] methods base >> >> other attached packages: >> [1] hgu95av2cdf_1.17.0 rat2302cdf_1.17.0 affyQCReport_1.15.2 >> [4] geneplotter_1.15.2 lattice_0.16-2 RColorBrewer_1.0-1 >> [7] affyPLM_1.13.6 affydata_1.11.2 simpleaffy_2.11.21 >> [10] affycoretools_1.9.2 annaffy_1.9.1 xtable_1.4-6 >> [13] gcrma_2.9.1 matchprobes_1.9.10 biomaRt_1.11.4 >> [16] RCurl_0.8-1 XML_1.9-0 GOstats_2.3.8 >> [19] Category_2.3.16 genefilter_1.15.3 survival_2.32 >> [22] KEGG_1.17.0 RBGL_1.13.3 annotate_1.15.2 >> [25] AnnotationDbi_0.0.83 RSQLite_0.6-0 DBI_0.2-3 >> [28] GO_1.17.0 graph_1.15.10 limma_2.11.9 >> [31] affy_1.15.7 preprocessCore_0.99.12 affyio_1.5.6 >> [34] Biobase_1.15.21 >> >> loaded via a namespace (and not attached): >> [1] cluster_1.11.7 grid_2.6.0 KernSmooth_2.22-20 >> >> > affy.batch.sub >> AffyBatch object >> size of arrays=834x834 features (14 kb) >> cdf=Rat230_2 (31099 affyids) >> number of samples=16 >> number of genes=31099 >> annotation=rat2302 >> notes= >> > QCReport(affy.batch.sub) >> Error in attr(groups, "names") <- names : >> 'names' attribute [16] must be the same length as the vector [1] >> >> Enter a frame number, or 0 to exit >> >> 1: QCReport(affy.batch.sub) >> 2: signalDist(object) >> 3: boxplot(object, names = ArrayIndex, ylab = "Log2(Intensity)", xlab >> = "Array >> 4: boxplot.default(object, names = ArrayIndex, ylab = >> "Log2(Intensity)", xlab >> >> Selection: 4 >> Called from: eval(expr, envir, enclos) >> Browse[1]> ls() >> [1] "add" "args" "at" "border" "col" >> [6] "groups" "horizontal" "log" "n" "namedargs" >> [11] "names" "notch" "outline" "pars" "plot" >> [16] "range" "*tmp*" "varwidth" "width" "x" >> Browse[1]> names >> [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" >> "14" "15" >> [16] "16" >> Browse[1]> names(group) >> NULL >> Browse[1]> names(groups) >> [1] "" >> Browse[1]> names(groups) <- names >> Error during wrapup: 'names' attribute [16] must be the same length as >> the vector [1] >> Browse[1]> >
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Hi Mark, Let's see if we cannot fix some of the problems and hopefully life will get better. Mark W Kimpel wrote: > Seth and Robert, > > Looks like I may have more than one problem. To clarify one point first, > in my original post I was using affy.batch.sub, which consisted of just > some of the arrays from my affy.batch. To make sure I'm not having a > problem with subsetting, in my subsequent posts I am using the affybatch > object created just today with ReadAffy. No old versions here, just what > comes out of my sessionInfo(). > > As you can see below, there may be a problem with my boxplot method but > also with the affybatch object. The latter is of class AffyBatch but is > not a valid object. > > Thanks, Mark > > > class(affy.batch) > [1] "AffyBatch" > attr(,"package") > [1] "affy" > > > require(affy) > > showMethods("boxplot") > Error in get(if (inherited) ".AllMTable" else ".MTable", envir = env) : > variable ".AllMTable" was not found there is something very odd about this - I have not seen it before, but it suggests that you might need to do a clean re-install of R and packages as something in the methods package (I think) is very confused. Not good news, I know, but you should not have this problem. And just to be sure this happens if you just start up R, load the affy library and then issue the commands above? That is what you need to check. Does this only happen for boxplot? What if you look at showMethods(exprs) or something of that nature? > > Enter a frame number, or 0 to exit > > 1: showMethods("boxplot") > 2: .showMethodsTable(getGeneric(f, where = where), includeDefs, > inherited, cla > 3: get(if (inherited) ".AllMTable" else ".MTable", envir = env) > > > > validObject(affy.batch) > Error in validObject(affy.batch) : > invalid class "AffyBatch" object: sampleNames differ between assayData > and phenoData This is a bit easier to fix. Simply change the sampleNames on one of the two structures to be the same as the others. Basically this is saying that the column names for your expression data do not agree with the row names of the phenotypic data. They might be different, or they might be out of order. You should look at both again using the AffyBatch example data: colnames(exprs(affybatch.example)) rownames(pData(affybatch.example)) need to be the same. If they are not then you need to figure out why not and fix them (maybe they are not in the same order, or one of them might be missing). I hope that helps Robert > > Enter a frame number, or 0 to exit > > 1: validObject(affy.batch) > > > par(mfrow=c(2, 1)) > > ArrayIndex = as.character(1:length(sampleNames(affy.batch))) > > > boxplot(affy.batch,names=ArrayIndex,ylab="Log2(Intensity)",xlab="Array > Index") > Error in attr(groups, "names") <- names : > 'names' attribute [80] must be the same length as the vector [1] > > Enter a frame number, or 0 to exit > > 1: boxplot(affy.batch, names = ArrayIndex, ylab = "Log2(Intensity)", > xlab = "A > 2: boxplot(affy.batch, names = ArrayIndex, ylab = "Log2(Intensity)", > xlab = "A > 3: boxplot.default(affy.batch, names = ArrayIndex, ylab = > "Log2(Intensity)", x > > Selection: > > --- > > Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry > Indiana University School of Medicine > > 15032 Hunter Court, Westfield, IN 46074 > > (317) 490-5129 Work, & Mobile & VoiceMail > (317) 663-0513 Home (no voice mail please) > > ****************************************************************** > > Robert Gentleman wrote: >> It looks to me like you are using a function named QCReport, not >> QAReport (and indeed there is no such thing - you might look at >> affyQAReport, which is in the same package but is very different). >> >> You can try to see what is happening by looking at the code from >> signalDist: >> >> par(mfrow=c(2, 1)) >> ArrayIndex = as.character(1:length(sampleNames(object))) >> boxplot(object,names=ArrayIndex,ylab="Log2(Intensity)",xlab="Array >> Index") >> >> >> where instead of object you use affy.batch.sub. The code looks pretty >> straightforward, so I don't know what the problem might be. It is a >> bit odd, it seems to me to use integers in place of the sample names... >> >> I used the affybatch.example and it worked for me.. ( one issue with >> that was >> Warning message: >> In data.row.names(row.names, rowsi, i) : >> some row.names duplicated: >> 2,26,51,76,101,126,151,176,201,226,251,276,301,326,351,376,401,426, 451,476,501,526,551,576,601,626,651,676,701,726,751,776,801,826, >> >> .... >> >> which we may need to look at). >> >> best wishes >> Robert >> >> >> Mark W Kimpel wrote: >>> I am running into an error when I run QAReport on an affybatch >>> object. Below is my sessionInfo and output. I am using the devel >>> versions of R and BioC, all newly updated. Please advise. >>> >>> Thanks, >>> Mark >>> >>> Browse[1]> sessionInfo() >>> R version 2.6.0 Under development (unstable) (2007-06-30 r42095) >>> i686-pc-linux-gnu >>> >>> locale: >>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=e n_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en _US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.U TF-8;LC_IDENTIFICATION=C >>> >>> >>> attached base packages: >>> [1] grDevices datasets splines graphics stats tools utils >>> [8] methods base >>> >>> other attached packages: >>> [1] hgu95av2cdf_1.17.0 rat2302cdf_1.17.0 affyQCReport_1.15.2 >>> [4] geneplotter_1.15.2 lattice_0.16-2 RColorBrewer_1.0-1 >>> [7] affyPLM_1.13.6 affydata_1.11.2 simpleaffy_2.11.21 >>> [10] affycoretools_1.9.2 annaffy_1.9.1 xtable_1.4-6 >>> [13] gcrma_2.9.1 matchprobes_1.9.10 biomaRt_1.11.4 >>> [16] RCurl_0.8-1 XML_1.9-0 GOstats_2.3.8 >>> [19] Category_2.3.16 genefilter_1.15.3 survival_2.32 >>> [22] KEGG_1.17.0 RBGL_1.13.3 annotate_1.15.2 >>> [25] AnnotationDbi_0.0.83 RSQLite_0.6-0 DBI_0.2-3 >>> [28] GO_1.17.0 graph_1.15.10 limma_2.11.9 >>> [31] affy_1.15.7 preprocessCore_0.99.12 affyio_1.5.6 >>> [34] Biobase_1.15.21 >>> >>> loaded via a namespace (and not attached): >>> [1] cluster_1.11.7 grid_2.6.0 KernSmooth_2.22-20 >>> >>> > affy.batch.sub >>> AffyBatch object >>> size of arrays=834x834 features (14 kb) >>> cdf=Rat230_2 (31099 affyids) >>> number of samples=16 >>> number of genes=31099 >>> annotation=rat2302 >>> notes= >>> > QCReport(affy.batch.sub) >>> Error in attr(groups, "names") <- names : >>> 'names' attribute [16] must be the same length as the vector [1] >>> >>> Enter a frame number, or 0 to exit >>> >>> 1: QCReport(affy.batch.sub) >>> 2: signalDist(object) >>> 3: boxplot(object, names = ArrayIndex, ylab = "Log2(Intensity)", xlab >>> = "Array >>> 4: boxplot.default(object, names = ArrayIndex, ylab = >>> "Log2(Intensity)", xlab >>> >>> Selection: 4 >>> Called from: eval(expr, envir, enclos) >>> Browse[1]> ls() >>> [1] "add" "args" "at" "border" "col" >>> [6] "groups" "horizontal" "log" "n" "namedargs" >>> [11] "names" "notch" "outline" "pars" "plot" >>> [16] "range" "*tmp*" "varwidth" "width" "x" >>> Browse[1]> names >>> [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" >>> "13" "14" "15" >>> [16] "16" >>> Browse[1]> names(group) >>> NULL >>> Browse[1]> names(groups) >>> [1] "" >>> Browse[1]> names(groups) <- names >>> Error during wrapup: 'names' attribute [16] must be the same length >>> as the vector [1] >>> Browse[1]> >> > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org
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I believe I have identified at least one potential contributor to the problem. In my .Rprofile, the very last like is "require(affycoretools)". I have this because affycoretools loads so many of the packages I use every day. When I start R without .Rprofile, QCReport works fine, but when I use .Rprofile, I get the following slew of error messages, which I sheepishly have to admit I have been ignoring because I wasn't having any problems. Of note is the lines: "The following object(s) are masked from package:affy : barplot," It looks to me like some of the base packages are loading after affy and this is causing problems. However, now that I have gotten QCReport to run, I am having trouble with affyQAReport. I am running R on a Linux machine with 4GB of RAM, and when I run affyQAReport on 80 rat2302 arrays I get an out of memory message. When I subset the affybatch down to 16 arrays, I get the following error "affyQAReport(affyB = affy.batch.sub, output = "pdf", outdir = "~/Genomics/TL01-05/affyQA", overwrite = FALSE, repName = "affyQAreport.pdf") Error in affyQAReport(affyB = affy.batch.sub, output = "pdf", outdir = "~/Genomics/TL01-05/affyQA", : could not find function "dist2" I agree that this is odd behavior. If you think I should reinstall R and packages, I'll do it. Below is the full output of my R startup if I have .Rprofile in play and load affycoretools on bootup. Mark R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. Loading required package: utils [1] "packages do not need updated" Loading required package: RSPerl Error in dyn.load(file, ...) : unable to load shared library '/home/mkimpel/R_HOME/R-devel/R-build/site- library/RSPerl/libs/RSPerl.so': /home/mkimpel/R_HOME/R-devel/R-build/site- library/RSPerl/libs/RSPerl.so: undefined symbol: Rf_initEmbeddedR In addition: There were 18 warnings (use warnings() to see them) sh: -c: line 0: syntax error near unexpected token `(' sh: -c: line 0: `./WriteXLS.pl --CSVpath=CSVFILES.tmp/ --CSVfiles=*.csv paste(oldwd, TestReport.xls, sep='/')' Loading required package: affycoretools Loading required package: affy Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: affyio Loading required package: preprocessCore Loading required package: limma Loading required package: GOstats Loading required package: graph Loading required package: GO Loading required package: annotate Loading required package: AnnotationDbi Loading required package: DBI Loading required package: RSQLite Loading required package: RBGL Loading required package: Category Loading required package: KEGG Loading required package: genefilter Loading required package: survival Loading required package: stats Attaching package: 'stats' The following object(s) are masked from package:affy : update Loading required package: graphics Attaching package: 'graphics' The following object(s) are masked from package:affy : barplot, boxplot, hist, image Loading required package: splines Loading required package: biomaRt Loading required package: XML Attaching package: 'XML' The following object(s) are masked from package:graph : addNode Loading required package: RCurl Attaching package: 'biomaRt' The following object(s) are masked from package:annotate : getGO Loading required package: gcrma Loading required package: matchprobes Loading required package: xtable Loading required package: annaffy Attaching package: 'affycoretools' The following object(s) are masked _by_ .GlobalEnv : vennCounts2, vennSelect > if(!exists("baseenv", mode="function")) baseenv <- function() NULL > options(STERM='iESS', editor='emacsclient') > --- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please) ****************************************************************** Robert Gentleman wrote: > Hi Mark, > > Let's see if we cannot fix some of the problems and hopefully life > will get better. > > > Mark W Kimpel wrote: >> Seth and Robert, >> >> Looks like I may have more than one problem. To clarify one point >> first, in my original post I was using affy.batch.sub, which consisted >> of just some of the arrays from my affy.batch. To make sure I'm not >> having a problem with subsetting, in my subsequent posts I am using >> the affybatch object created just today with ReadAffy. No old versions >> here, just what comes out of my sessionInfo(). >> >> As you can see below, there may be a problem with my boxplot method >> but also with the affybatch object. The latter is of class AffyBatch >> but is not a valid object. >> >> Thanks, Mark >> >> > class(affy.batch) >> [1] "AffyBatch" >> attr(,"package") >> [1] "affy" >> >> > require(affy) >> > showMethods("boxplot") >> Error in get(if (inherited) ".AllMTable" else ".MTable", envir = env) : >> variable ".AllMTable" was not found > > there is something very odd about this - I have not seen it before, > but it suggests that you might need to do a clean re-install of R and > packages as something in the methods package (I think) is very confused. > Not good news, I know, but you should not have this problem. And just to > be sure this happens if you just start up R, load the affy library and > then issue the commands above? That is what you need to check. > > > Does this only happen for boxplot? What if you look at > showMethods(exprs) or something of that nature? > >> >> Enter a frame number, or 0 to exit >> >> 1: showMethods("boxplot") >> 2: .showMethodsTable(getGeneric(f, where = where), includeDefs, >> inherited, cla >> 3: get(if (inherited) ".AllMTable" else ".MTable", envir = env) >> >> >> > validObject(affy.batch) >> Error in validObject(affy.batch) : >> invalid class "AffyBatch" object: sampleNames differ between >> assayData and phenoData > > This is a bit easier to fix. Simply change the sampleNames on one of > the two structures to be the same as the others. > > Basically this is saying that the column names for your expression > data do not agree with the row names of the phenotypic data. They might > be different, or they might be out of order. You should look at both > again using the AffyBatch example data: > > colnames(exprs(affybatch.example)) > rownames(pData(affybatch.example)) > > need to be the same. If they are not then you need to figure out why > not and fix them (maybe they are not in the same order, or one of them > might be missing). > > I hope that helps > > Robert > >> >> Enter a frame number, or 0 to exit >> >> 1: validObject(affy.batch) >> >> > par(mfrow=c(2, 1)) >> > ArrayIndex = as.character(1:length(sampleNames(affy.batch))) >> > >> boxplot(affy.batch,names=ArrayIndex,ylab="Log2(Intensity)",xlab="Array >> Index") >> Error in attr(groups, "names") <- names : >> 'names' attribute [80] must be the same length as the vector [1] >> >> Enter a frame number, or 0 to exit >> >> 1: boxplot(affy.batch, names = ArrayIndex, ylab = "Log2(Intensity)", >> xlab = "A >> 2: boxplot(affy.batch, names = ArrayIndex, ylab = "Log2(Intensity)", >> xlab = "A >> 3: boxplot.default(affy.batch, names = ArrayIndex, ylab = >> "Log2(Intensity)", x >> >> Selection: >> >> --- >> >> Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry >> Indiana University School of Medicine >> >> 15032 Hunter Court, Westfield, IN 46074 >> >> (317) 490-5129 Work, & Mobile & VoiceMail >> (317) 663-0513 Home (no voice mail please) >> >> ****************************************************************** >> >> Robert Gentleman wrote: >>> It looks to me like you are using a function named QCReport, not >>> QAReport (and indeed there is no such thing - you might look at >>> affyQAReport, which is in the same package but is very different). >>> >>> You can try to see what is happening by looking at the code from >>> signalDist: >>> >>> par(mfrow=c(2, 1)) >>> ArrayIndex = as.character(1:length(sampleNames(object))) >>> boxplot(object,names=ArrayIndex,ylab="Log2(Intensity)",xlab="Array >>> Index") >>> >>> >>> where instead of object you use affy.batch.sub. The code looks pretty >>> straightforward, so I don't know what the problem might be. It is a >>> bit odd, it seems to me to use integers in place of the sample names... >>> >>> I used the affybatch.example and it worked for me.. ( one issue with >>> that was >>> Warning message: >>> In data.row.names(row.names, rowsi, i) : >>> some row.names duplicated: >>> 2,26,51,76,101,126,151,176,201,226,251,276,301,326,351,376,401,426 ,451,476,501,526,551,576,601,626,651,676,701,726,751,776,801,826, >>> >>> .... >>> >>> which we may need to look at). >>> >>> best wishes >>> Robert >>> >>> >>> Mark W Kimpel wrote: >>>> I am running into an error when I run QAReport on an affybatch >>>> object. Below is my sessionInfo and output. I am using the devel >>>> versions of R and BioC, all newly updated. Please advise. >>>> >>>> Thanks, >>>> Mark >>>> >>>> Browse[1]> sessionInfo() >>>> R version 2.6.0 Under development (unstable) (2007-06-30 r42095) >>>> i686-pc-linux-gnu >>>> >>>> locale: >>>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE= en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=e n_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US. UTF-8;LC_IDENTIFICATION=C >>>> >>>> >>>> attached base packages: >>>> [1] grDevices datasets splines graphics stats tools utils >>>> [8] methods base >>>> >>>> other attached packages: >>>> [1] hgu95av2cdf_1.17.0 rat2302cdf_1.17.0 affyQCReport_1.15.2 >>>> [4] geneplotter_1.15.2 lattice_0.16-2 RColorBrewer_1.0-1 >>>> [7] affyPLM_1.13.6 affydata_1.11.2 simpleaffy_2.11.21 >>>> [10] affycoretools_1.9.2 annaffy_1.9.1 xtable_1.4-6 >>>> [13] gcrma_2.9.1 matchprobes_1.9.10 biomaRt_1.11.4 >>>> [16] RCurl_0.8-1 XML_1.9-0 GOstats_2.3.8 >>>> [19] Category_2.3.16 genefilter_1.15.3 survival_2.32 >>>> [22] KEGG_1.17.0 RBGL_1.13.3 annotate_1.15.2 >>>> [25] AnnotationDbi_0.0.83 RSQLite_0.6-0 DBI_0.2-3 >>>> [28] GO_1.17.0 graph_1.15.10 limma_2.11.9 >>>> [31] affy_1.15.7 preprocessCore_0.99.12 affyio_1.5.6 >>>> [34] Biobase_1.15.21 >>>> >>>> loaded via a namespace (and not attached): >>>> [1] cluster_1.11.7 grid_2.6.0 KernSmooth_2.22-20 >>>> >>>> > affy.batch.sub >>>> AffyBatch object >>>> size of arrays=834x834 features (14 kb) >>>> cdf=Rat230_2 (31099 affyids) >>>> number of samples=16 >>>> number of genes=31099 >>>> annotation=rat2302 >>>> notes= >>>> > QCReport(affy.batch.sub) >>>> Error in attr(groups, "names") <- names : >>>> 'names' attribute [16] must be the same length as the vector [1] >>>> >>>> Enter a frame number, or 0 to exit >>>> >>>> 1: QCReport(affy.batch.sub) >>>> 2: signalDist(object) >>>> 3: boxplot(object, names = ArrayIndex, ylab = "Log2(Intensity)", >>>> xlab = "Array >>>> 4: boxplot.default(object, names = ArrayIndex, ylab = >>>> "Log2(Intensity)", xlab >>>> >>>> Selection: 4 >>>> Called from: eval(expr, envir, enclos) >>>> Browse[1]> ls() >>>> [1] "add" "args" "at" "border" "col" >>>> [6] "groups" "horizontal" "log" "n" "namedargs" >>>> [11] "names" "notch" "outline" "pars" "plot" >>>> [16] "range" "*tmp*" "varwidth" "width" "x" >>>> Browse[1]> names >>>> [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" >>>> "13" "14" "15" >>>> [16] "16" >>>> Browse[1]> names(group) >>>> NULL >>>> Browse[1]> names(groups) >>>> [1] "" >>>> Browse[1]> names(groups) <- names >>>> Error during wrapup: 'names' attribute [16] must be the same length >>>> as the vector [1] >>>> Browse[1]> >>> >> >
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Hi, Mark W Kimpel wrote: > I believe I have identified at least one potential contributor to the > problem. In my .Rprofile, the very last like is > "require(affycoretools)". I have this because affycoretools loads so > many of the packages I use every day. When I start R without .Rprofile, > QCReport works fine, but when I use .Rprofile, I get the following slew > of error messages, which I sheepishly have to admit I have been ignoring > because I wasn't having any problems. Of note is the lines: > > "The following object(s) are masked from package:affy : > > barplot," > > It looks to me like some of the base packages are loading after affy and > this is causing problems. Ignoring error/warning messages is really your call, but please do include such information with your initial post - it is kind of important for those of us trying to figure out what has gone wrong. And yes, that does seem to be a part of the problem. You can, and probably should explicitly load the base packages before any others and that should help sort out the masking. > > However, now that I have gotten QCReport to run, I am having trouble > with affyQAReport. I am running R on a Linux machine with 4GB of RAM, > and when I run affyQAReport on 80 rat2302 arrays I get an out of memory > message. When I subset the affybatch down to 16 arrays, I get the > following error Tracking down the memory issue will be harder - basically there are some inefficiencies, but I am not just sure where they might be. If you could run this with options(error=recover) and give some info on where in the computations it is happening that would help - but a quicker fix is going to be more RAM, I think. > > "affyQAReport(affyB = affy.batch.sub, output = "pdf", outdir = > "~/Genomics/TL01-05/affyQA", overwrite = FALSE, repName = > "affyQAreport.pdf") > > Error in affyQAReport(affyB = affy.batch.sub, output = "pdf", outdir = > "~/Genomics/TL01-05/affyQA", : > could not find function "dist2" This was what I had expected - a bug in genefilter that I finally tracked down on Friday - I think that if you do an update.packages now you will see that you get a new version, and that this error message will go away. > > I agree that this is odd behavior. If you think I should reinstall R and > packages, I'll do it. Below is the full output of my R startup if I have > .Rprofile in play and load affycoretools on bootup. no things should be a bit better now > > Mark > > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > > Loading required package: utils > [1] "packages do not need updated" > Loading required package: RSPerl > Error in dyn.load(file, ...) : > unable to load shared library > '/home/mkimpel/R_HOME/R-devel/R-build/site- library/RSPerl/libs/RSPerl.so': > > /home/mkimpel/R_HOME/R-devel/R-build/site- library/RSPerl/libs/RSPerl.so: > undefined symbol: Rf_initEmbeddedR > In addition: There were 18 warnings (use warnings() to see them) > sh: -c: line 0: syntax error near unexpected token `(' > sh: -c: line 0: `./WriteXLS.pl --CSVpath=CSVFILES.tmp/ --CSVfiles=*.csv This is worth reporting to the maintainer of RSPerl > paste(oldwd, TestReport.xls, sep='/')' > Loading required package: affycoretools > Loading required package: affy > Loading required package: Biobase > Loading required package: tools > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > Loading required package: affyio > Loading required package: preprocessCore > Loading required package: limma > Loading required package: GOstats > Loading required package: graph > Loading required package: GO > Loading required package: annotate > Loading required package: AnnotationDbi > Loading required package: DBI > Loading required package: RSQLite > Loading required package: RBGL > Loading required package: Category > Loading required package: KEGG > Loading required package: genefilter > Loading required package: survival > Loading required package: stats > > Attaching package: 'stats' > > > The following object(s) are masked from package:affy : > > update > > Loading required package: graphics > > Attaching package: 'graphics' > > > The following object(s) are masked from package:affy : > > barplot, > boxplot, > hist, > image > > Loading required package: splines > Loading required package: biomaRt > Loading required package: XML > > Attaching package: 'XML' > > > The following object(s) are masked from package:graph : > > addNode > > Loading required package: RCurl > > Attaching package: 'biomaRt' > > > The following object(s) are masked from package:annotate : > > getGO > > Loading required package: gcrma > Loading required package: matchprobes > Loading required package: xtable > Loading required package: annaffy > > Attaching package: 'affycoretools' > > > The following object(s) are masked _by_ .GlobalEnv : > > vennCounts2, > vennSelect > > > if(!exists("baseenv", mode="function")) baseenv <- function() NULL > > options(STERM='iESS', editor='emacsclient') > > > > --- > > Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry > Indiana University School of Medicine > > 15032 Hunter Court, Westfield, IN 46074 > > (317) 490-5129 Work, & Mobile & VoiceMail > (317) 663-0513 Home (no voice mail please) > > ****************************************************************** > > Robert Gentleman wrote: >> Hi Mark, >> >> Let's see if we cannot fix some of the problems and hopefully life >> will get better. >> >> >> Mark W Kimpel wrote: >>> Seth and Robert, >>> >>> Looks like I may have more than one problem. To clarify one point >>> first, in my original post I was using affy.batch.sub, which >>> consisted of just some of the arrays from my affy.batch. To make sure >>> I'm not having a problem with subsetting, in my subsequent posts I am >>> using the affybatch object created just today with ReadAffy. No old >>> versions here, just what comes out of my sessionInfo(). >>> >>> As you can see below, there may be a problem with my boxplot method >>> but also with the affybatch object. The latter is of class AffyBatch >>> but is not a valid object. >>> >>> Thanks, Mark >>> >>> > class(affy.batch) >>> [1] "AffyBatch" >>> attr(,"package") >>> [1] "affy" >>> >>> > require(affy) >>> > showMethods("boxplot") >>> Error in get(if (inherited) ".AllMTable" else ".MTable", envir = env) : >>> variable ".AllMTable" was not found >> >> there is something very odd about this - I have not seen it before, >> but it suggests that you might need to do a clean re-install of R and >> packages as something in the methods package (I think) is very confused. >> Not good news, I know, but you should not have this problem. And just >> to be sure this happens if you just start up R, load the affy library >> and then issue the commands above? That is what you need to check. >> >> >> Does this only happen for boxplot? What if you look at >> showMethods(exprs) or something of that nature? >> >>> >>> Enter a frame number, or 0 to exit >>> >>> 1: showMethods("boxplot") >>> 2: .showMethodsTable(getGeneric(f, where = where), includeDefs, >>> inherited, cla >>> 3: get(if (inherited) ".AllMTable" else ".MTable", envir = env) >>> >>> >>> > validObject(affy.batch) >>> Error in validObject(affy.batch) : >>> invalid class "AffyBatch" object: sampleNames differ between >>> assayData and phenoData >> >> This is a bit easier to fix. Simply change the sampleNames on one of >> the two structures to be the same as the others. >> >> Basically this is saying that the column names for your expression >> data do not agree with the row names of the phenotypic data. They >> might be different, or they might be out of order. You should look at >> both >> again using the AffyBatch example data: >> >> colnames(exprs(affybatch.example)) >> rownames(pData(affybatch.example)) >> >> need to be the same. If they are not then you need to figure out why >> not and fix them (maybe they are not in the same order, or one of them >> might be missing). >> >> I hope that helps >> >> Robert >> >>> >>> Enter a frame number, or 0 to exit >>> >>> 1: validObject(affy.batch) >>> >>> > par(mfrow=c(2, 1)) >>> > ArrayIndex = as.character(1:length(sampleNames(affy.batch))) >>> > >>> boxplot(affy.batch,names=ArrayIndex,ylab="Log2(Intensity)",xlab="Array >>> Index") >>> Error in attr(groups, "names") <- names : >>> 'names' attribute [80] must be the same length as the vector [1] >>> >>> Enter a frame number, or 0 to exit >>> >>> 1: boxplot(affy.batch, names = ArrayIndex, ylab = "Log2(Intensity)", >>> xlab = "A >>> 2: boxplot(affy.batch, names = ArrayIndex, ylab = "Log2(Intensity)", >>> xlab = "A >>> 3: boxplot.default(affy.batch, names = ArrayIndex, ylab = >>> "Log2(Intensity)", x >>> >>> Selection: >>> >>> --- >>> >>> Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry >>> Indiana University School of Medicine >>> >>> 15032 Hunter Court, Westfield, IN 46074 >>> >>> (317) 490-5129 Work, & Mobile & VoiceMail >>> (317) 663-0513 Home (no voice mail please) >>> >>> ****************************************************************** >>> >>> Robert Gentleman wrote: >>>> It looks to me like you are using a function named QCReport, not >>>> QAReport (and indeed there is no such thing - you might look at >>>> affyQAReport, which is in the same package but is very different). >>>> >>>> You can try to see what is happening by looking at the code from >>>> signalDist: >>>> >>>> par(mfrow=c(2, 1)) >>>> ArrayIndex = as.character(1:length(sampleNames(object))) >>>> boxplot(object,names=ArrayIndex,ylab="Log2(Intensity)",xlab="Array >>>> Index") >>>> >>>> >>>> where instead of object you use affy.batch.sub. The code looks >>>> pretty straightforward, so I don't know what the problem might be. >>>> It is a bit odd, it seems to me to use integers in place of the >>>> sample names... >>>> >>>> I used the affybatch.example and it worked for me.. ( one issue with >>>> that was >>>> Warning message: >>>> In data.row.names(row.names, rowsi, i) : >>>> some row.names duplicated: >>>> 2,26,51,76,101,126,151,176,201,226,251,276,301,326,351,376,401,42 6,451,476,501,526,551,576,601,626,651,676,701,726,751,776,801,826, >>>> >>>> .... >>>> >>>> which we may need to look at). >>>> >>>> best wishes >>>> Robert >>>> >>>> >>>> Mark W Kimpel wrote: >>>>> I am running into an error when I run QAReport on an affybatch >>>>> object. Below is my sessionInfo and output. I am using the devel >>>>> versions of R and BioC, all newly updated. Please advise. >>>>> >>>>> Thanks, >>>>> Mark >>>>> >>>>> Browse[1]> sessionInfo() >>>>> R version 2.6.0 Under development (unstable) (2007-06-30 r42095) >>>>> i686-pc-linux-gnu >>>>> >>>>> locale: >>>>> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE =en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER= en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US .UTF-8;LC_IDENTIFICATION=C >>>>> >>>>> >>>>> attached base packages: >>>>> [1] grDevices datasets splines graphics stats tools utils >>>>> [8] methods base >>>>> >>>>> other attached packages: >>>>> [1] hgu95av2cdf_1.17.0 rat2302cdf_1.17.0 >>>>> affyQCReport_1.15.2 >>>>> [4] geneplotter_1.15.2 lattice_0.16-2 RColorBrewer_1.0-1 >>>>> [7] affyPLM_1.13.6 affydata_1.11.2 simpleaffy_2.11.21 >>>>> [10] affycoretools_1.9.2 annaffy_1.9.1 xtable_1.4-6 >>>>> [13] gcrma_2.9.1 matchprobes_1.9.10 biomaRt_1.11.4 >>>>> [16] RCurl_0.8-1 XML_1.9-0 GOstats_2.3.8 >>>>> [19] Category_2.3.16 genefilter_1.15.3 survival_2.32 >>>>> [22] KEGG_1.17.0 RBGL_1.13.3 annotate_1.15.2 >>>>> [25] AnnotationDbi_0.0.83 RSQLite_0.6-0 DBI_0.2-3 >>>>> [28] GO_1.17.0 graph_1.15.10 limma_2.11.9 >>>>> [31] affy_1.15.7 preprocessCore_0.99.12 affyio_1.5.6 >>>>> [34] Biobase_1.15.21 >>>>> >>>>> loaded via a namespace (and not attached): >>>>> [1] cluster_1.11.7 grid_2.6.0 KernSmooth_2.22-20 >>>>> >>>>> > affy.batch.sub >>>>> AffyBatch object >>>>> size of arrays=834x834 features (14 kb) >>>>> cdf=Rat230_2 (31099 affyids) >>>>> number of samples=16 >>>>> number of genes=31099 >>>>> annotation=rat2302 >>>>> notes= >>>>> > QCReport(affy.batch.sub) >>>>> Error in attr(groups, "names") <- names : >>>>> 'names' attribute [16] must be the same length as the vector [1] >>>>> >>>>> Enter a frame number, or 0 to exit >>>>> >>>>> 1: QCReport(affy.batch.sub) >>>>> 2: signalDist(object) >>>>> 3: boxplot(object, names = ArrayIndex, ylab = "Log2(Intensity)", >>>>> xlab = "Array >>>>> 4: boxplot.default(object, names = ArrayIndex, ylab = >>>>> "Log2(Intensity)", xlab >>>>> >>>>> Selection: 4 >>>>> Called from: eval(expr, envir, enclos) >>>>> Browse[1]> ls() >>>>> [1] "add" "args" "at" "border" "col" >>>>> [6] "groups" "horizontal" "log" "n" "namedargs" >>>>> [11] "names" "notch" "outline" "pars" "plot" >>>>> [16] "range" "*tmp*" "varwidth" "width" "x" >>>>> Browse[1]> names >>>>> [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" >>>>> "13" "14" "15" >>>>> [16] "16" >>>>> Browse[1]> names(group) >>>>> NULL >>>>> Browse[1]> names(groups) >>>>> [1] "" >>>>> Browse[1]> names(groups) <- names >>>>> Error during wrapup: 'names' attribute [16] must be the same length >>>>> as the vector [1] >>>>> Browse[1]> >>>> >>> >> > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 6.6 years ago
Robert Gentleman <rgentlem at="" fhcrc.org=""> writes: > Mark W Kimpel wrote: >> Robert, >> >> You are correct, I am using the function QCReport. I downloaded the >> source code of the packages affy and affyQCReport and believe the >> problem may be that the wrong method is being called when boxplot is >> invoked on my affybatch object. I get an error when I do >> signature(affy.batch). See below... Is this expected behavior? Could my >> affybatch object be corrupted? Mark One thing to try, in addition to Robert's suggestions, is: validObject(affy.batch) And if you determine that you might have an instance restored from an old version of R/BioC, then you might take a look at the updateObject method which will try to update your object to the latest class definition (works in most, but probably not all cases). + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center BioC: http://bioconductor.org/ Blog: http://userprimary.net/user/
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 6.6 years ago
Robert Gentleman <rgentlem at="" fhcrc.org=""> writes: > Mark W Kimpel wrote: >> Robert, >> >> You are correct, I am using the function QCReport. I downloaded the >> source code of the packages affy and affyQCReport and believe the >> problem may be that the wrong method is being called when boxplot is >> invoked on my affybatch object. I get an error when I do >> signature(affy.batch). See below... Is this expected behavior? Could my >> affybatch object be corrupted? Mark One thing to try, in addition to Robert's suggestions, is: validObject(affy.batch) And if you determine that you might have an instance restored from an old version of R/BioC, then you might take a look at the updateObject method which will try to update your object to the latest class definition (works in most, but probably not all cases). + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center BioC: http://bioconductor.org/ Blog: http://userprimary.net/user/
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