arrayQualityMetrics Error
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Ramzi TEMANNI ▴ 160
@ramzi-temanni-3819
Last seen 8.2 years ago
Hi, I'm runing some QC analysis with 5 Affy mouse genechip HT430PM I've installed the required libraries(affy, arrayQualityMetrics, htmg430pmcdf) and all dependecies I'm using the following code: fls <- list.files("/", ".*CEL") eset <- justRMA(filenames = fls) aBatch <- ReadAffy(filenames = fls) arrayQualityMetrics(aBatch,outdir = "report") The last commad shows the following error message: The report will be written in directory 'report'. Error in setQCEnvironment(cdfn) : Could not find array definition file ' htmg430pmcdf.qcdef '. Simpleaffy does not know the QC parameters for this array type. See the package vignette for details about how to specify QC parameters manually. Error in density.default(as.matrix(log2(mm(expressionset))), ...) : 'x' contains missing values In addition: Warning message: In aqm.qcstats(expressionset) : 'plot(qcStats)' from the package 'simpleaffy' failed for this dataset. Error in obj[[i]]$legend : $ operator is invalid for atomic vectors In addition: Warning message: In arrayQualityMetrics(aBatch, outdir = "report") : Cannot draw the Perfect Match versus MisMatch plot Any idea about the orgin of this error ? Thanks in advance for your help. Kind regards Ramzi ---------------------------------------------------------------- > sessionInfo() R version 2.10.1 (2009-12-14) x86_64-pc-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] arrayQualityMetrics_2.4.3 affyPLM_1.22.0 [3] preprocessCore_1.8.0 gcrma_2.18.0 [5] htmg430pmcdf_2.5.0 affy_1.24.2 [7] Biobase_2.6.1 loaded via a namespace (and not attached): [1] affyio_1.14.0 annotate_1.24.0 AnnotationDbi_1.8.1 [4] beadarray_1.14.0 Biostrings_2.14.8 DBI_0.2-4 [7] genefilter_1.28.2 grid_2.10.1 hwriter_1.1 [10] IRanges_1.4.9 lattice_0.17-26 latticeExtra_0.6-4 [13] limma_3.2.1 marray_1.24.0 RColorBrewer_1.0-2 [16] RSQLite_0.7-3 simpleaffy_2.22.0 splines_2.10.1 [19] stats4_2.10.1 survival_2.35-8 tcltk_2.10.1 [22] tools_2.10.1 vsn_3.14.0 xtable_1.5-6 [[alternative HTML version deleted]]
cdf affy arrayQualityMetrics cdf affy arrayQualityMetrics • 1.4k views
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@james-w-macdonald-5106
Last seen 16 minutes ago
United States
Hi Ramzi, Ramzi TEMANNI wrote: > Hi, > I'm runing some QC analysis with 5 Affy mouse genechip HT430PM > I've installed the required libraries(affy, arrayQualityMetrics, > htmg430pmcdf) and all dependecies > I'm using the following code: > fls <- list.files("/", ".*CEL") > eset <- justRMA(filenames = fls) > aBatch <- ReadAffy(filenames = fls) > arrayQualityMetrics(aBatch,outdir = "report") > > The last commad shows the following error message: > > The report will be written in directory 'report'. > Error in setQCEnvironment(cdfn) : > Could not find array definition file ' htmg430pmcdf.qcdef '. Simpleaffy > does not know the QC parameters for this array type. > See the package vignette for details about how to specify QC parameters > manually. This seems pretty clear to me. The simpleaffy package does not have the QC parameters for this array and there is some explanation of how to fix this in the package vignette. Did you look in the package vignette to see how to fix it? Note that the htmg430pm chip is quite similar to the moe430 chip, so the QC parameters will likely be the same, but you might need to adjust the names of the QC probes. Best, Jim > > Error in density.default(as.matrix(log2(mm(expressionset))), ...) : > 'x' contains missing values > In addition: Warning message: > In aqm.qcstats(expressionset) : > 'plot(qcStats)' from the package 'simpleaffy' failed for this dataset. > Error in obj[[i]]$legend : $ operator is invalid for atomic vectors > In addition: Warning message: > In arrayQualityMetrics(aBatch, outdir = "report") : > Cannot draw the Perfect Match versus MisMatch plot > > Any idea about the orgin of this error ? > Thanks in advance for your help. > Kind regards > Ramzi > ---------------------------------------------------------------- > >> sessionInfo() > R version 2.10.1 (2009-12-14) > x86_64-pc-linux-gnu > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > attached base packages: > [1] stats graphics grDevices utils datasets methods base > other attached packages: > [1] arrayQualityMetrics_2.4.3 affyPLM_1.22.0 > [3] preprocessCore_1.8.0 gcrma_2.18.0 > [5] htmg430pmcdf_2.5.0 affy_1.24.2 > [7] Biobase_2.6.1 > loaded via a namespace (and not attached): > [1] affyio_1.14.0 annotate_1.24.0 AnnotationDbi_1.8.1 > [4] beadarray_1.14.0 Biostrings_2.14.8 DBI_0.2-4 > [7] genefilter_1.28.2 grid_2.10.1 hwriter_1.1 > [10] IRanges_1.4.9 lattice_0.17-26 latticeExtra_0.6-4 > [13] limma_3.2.1 marray_1.24.0 RColorBrewer_1.0-2 > [16] RSQLite_0.7-3 simpleaffy_2.22.0 splines_2.10.1 > [19] stats4_2.10.1 survival_2.35-8 tcltk_2.10.1 > [22] tools_2.10.1 vsn_3.14.0 xtable_1.5-6 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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Hi Jim, Thanks for your answer, it's my first experience with Affy data, I used to work with Agilent before. I take a look at the vignette and generated the requested file based on the info about the htmg430pm data : array htmg430pmcdf alpha1 0.05 alpha2 0.065 spk bioB AFFX-r2-Ec-bioB-3_at spk bioC AFFX-r2-Ec-bioC-3_at spk bioD AFFX-r2-Ec-bioD-3_at spk creX AFFX-r2-P1-cre-3_at ratio actin3/actin5 AFFX-b-ActinMur/M12481_3_at AFFX-b-ActinMur/M12481_5_at ratio actin3/actinM AFFX-b-ActinMur/M12481_3_at AFFX-b-ActinMur/M12481_M_at ratio gapdh3/gapdh5 AFFX-GapdhMur/M32599_3_at AFFX- GapdhMur/M32599_5_at ratio gapdh3/gapdhM AFFX-GapdhMur/M32599_3_at AFFX- GapdhMur/M32599_M_at report works well for normalized data, but for raw data i get the following errors: The report will be written in directory 'report'. Error : NAs in foreign function call (arg 1) Error in density.default(as.matrix(log2(mm(expressionset))), ...) : 'x' contains missing values In addition: Warning message: In aqm.qcstats(expressionset) : 'plot(qcStats)' from the package 'simpleaffy' failed for this dataset. Error in obj[[i]]$legend : $ operator is invalid for atomic vectors In addition: Warning message: In arrayQualityMetrics(aBatch, outdir = "report") : Cannot draw the Perfect Match versus MisMatch plot here's the code i'm using : # Identify CEL files. fls <- list.files("/", ".*CEL") # Input raw data aBatch <- ReadAffy(filenames = fls) # Process CEL files using RMA (robust multi-array average). eset <- justRMA(filenames = fls) arrayQualityMetrics(aBatch,outdir = "report_raw") arrayQualityMetrics(eset,outdir = "report_normalized") Any idea about what is wrong with the QC report on raw data ? Thanks in advance. Regards, Ramzi Best, Ramzi ---------------------------------------------------------------- On Mon, Jan 11, 2010 at 2:52 PM, James W. MacDonald <jmacdon@med.umich.edu>wrote: > Hi Ramzi, > > > Ramzi TEMANNI wrote: > >> Hi, >> I'm runing some QC analysis with 5 Affy mouse genechip HT430PM >> I've installed the required libraries(affy, arrayQualityMetrics, >> htmg430pmcdf) and all dependecies >> I'm using the following code: >> fls <- list.files("/", ".*CEL") >> eset <- justRMA(filenames = fls) >> aBatch <- ReadAffy(filenames = fls) >> arrayQualityMetrics(aBatch,outdir = "report") >> >> The last commad shows the following error message: >> >> The report will be written in directory 'report'. >> Error in setQCEnvironment(cdfn) : >> Could not find array definition file ' htmg430pmcdf.qcdef '. Simpleaffy >> does not know the QC parameters for this array type. >> See the package vignette for details about how to specify QC parameters >> manually. >> > > This seems pretty clear to me. The simpleaffy package does not have the QC > parameters for this array and there is some explanation of how to fix this > in the package vignette. Did you look in the package vignette to see how to > fix it? > > Note that the htmg430pm chip is quite similar to the moe430 chip, so the QC > parameters will likely be the same, but you might need to adjust the names > of the QC probes. > > Best, > > Jim > > >> Error in density.default(as.matrix(log2(mm(expressionset))), ...) : >> 'x' contains missing values >> In addition: Warning message: >> In aqm.qcstats(expressionset) : >> 'plot(qcStats)' from the package 'simpleaffy' failed for this dataset. >> Error in obj[[i]]$legend : $ operator is invalid for atomic vectors >> In addition: Warning message: >> In arrayQualityMetrics(aBatch, outdir = "report") : >> Cannot draw the Perfect Match versus MisMatch plot >> >> Any idea about the orgin of this error ? >> Thanks in advance for your help. >> Kind regards >> Ramzi >> ---------------------------------------------------------------- >> >> sessionInfo() >>> >> R version 2.10.1 (2009-12-14) >> x86_64-pc-linux-gnu >> locale: >> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C >> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 >> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 >> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C >> [9] LC_ADDRESS=C LC_TELEPHONE=C >> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> other attached packages: >> [1] arrayQualityMetrics_2.4.3 affyPLM_1.22.0 >> [3] preprocessCore_1.8.0 gcrma_2.18.0 >> [5] htmg430pmcdf_2.5.0 affy_1.24.2 >> [7] Biobase_2.6.1 >> loaded via a namespace (and not attached): >> [1] affyio_1.14.0 annotate_1.24.0 AnnotationDbi_1.8.1 >> [4] beadarray_1.14.0 Biostrings_2.14.8 DBI_0.2-4 >> [7] genefilter_1.28.2 grid_2.10.1 hwriter_1.1 >> [10] IRanges_1.4.9 lattice_0.17-26 latticeExtra_0.6-4 >> [13] limma_3.2.1 marray_1.24.0 RColorBrewer_1.0-2 >> [16] RSQLite_0.7-3 simpleaffy_2.22.0 splines_2.10.1 >> [19] stats4_2.10.1 survival_2.35-8 tcltk_2.10.1 >> [22] tools_2.10.1 vsn_3.14.0 xtable_1.5-6 >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > -- > James W. MacDonald, M.S. > Biostatistician > Douglas Lab > University of Michigan > Department of Human Genetics > 5912 Buhl > 1241 E. Catherine St. > Ann Arbor MI 48109-5618 > 734-615-7826 > ********************************************************** > Electronic Mail is not secure, may not be read every day, and should not be > used for urgent or sensitive issues > [[alternative HTML version deleted]]
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@groot-philip-de-1307
Last seen 8.2 years ago
Hello all, Please note that MAS5 won't work for PM-only arrays! So creating your own .qcdef file is pretty useless here... Regards, Dr. Philip de Groot Ph.D. Bioinformatics Researcher Wageningen University / TIFN Nutrigenomics Consortium Nutrition, Metabolism & Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: Erfelijkheidsleer: De Valk, Building 304 Dreijenweg 2, 6703 HA Wageningen Room: 0052a T: +31-317-485786 F: +31-317-483342 E-mail: Philip.deGroot at wur.nl <mailto:philip.degroot at="" wur.nl=""> Internet: http://www.nutrigenomicsconsortium.nl <http: www.nutrigenomicsconsortium.nl=""/> http://humannutrition.wur.nl <http: humannutrition.wur.nl=""/> https://madmax.bioinformatics.nl <https: madmax.bioinformatics.nl=""/> ________________________________ From: James W. MacDonald [mailto:jmacdon@med.umich.edu] Sent: Mon 11-1-2010 14:52 To: Ramzi TEMANNI Cc: Bioconductor Newsgroup Subject: Re: [BioC] arrayQualityMetrics Error Hi Ramzi, Ramzi TEMANNI wrote: > Hi, > I'm runing some QC analysis with 5 Affy mouse genechip HT430PM > I've installed the required libraries(affy, arrayQualityMetrics, > htmg430pmcdf) and all dependecies > I'm using the following code: > fls <- list.files("/", ".*CEL") > eset <- justRMA(filenames = fls) > aBatch <- ReadAffy(filenames = fls) > arrayQualityMetrics(aBatch,outdir = "report") > > The last commad shows the following error message: > > The report will be written in directory 'report'. > Error in setQCEnvironment(cdfn) : > Could not find array definition file ' htmg430pmcdf.qcdef '. Simpleaffy > does not know the QC parameters for this array type. > See the package vignette for details about how to specify QC parameters > manually. This seems pretty clear to me. The simpleaffy package does not have the QC parameters for this array and there is some explanation of how to fix this in the package vignette. Did you look in the package vignette to see how to fix it? Note that the htmg430pm chip is quite similar to the moe430 chip, so the QC parameters will likely be the same, but you might need to adjust the names of the QC probes. Best, Jim > > Error in density.default(as.matrix(log2(mm(expressionset))), ...) : > 'x' contains missing values > In addition: Warning message: > In aqm.qcstats(expressionset) : > 'plot(qcStats)' from the package 'simpleaffy' failed for this dataset. > Error in obj[[i]]$legend : $ operator is invalid for atomic vectors > In addition: Warning message: > In arrayQualityMetrics(aBatch, outdir = "report") : > Cannot draw the Perfect Match versus MisMatch plot > > Any idea about the orgin of this error ? > Thanks in advance for your help. > Kind regards > Ramzi > ---------------------------------------------------------------- > >> sessionInfo() > R version 2.10.1 (2009-12-14) > x86_64-pc-linux-gnu > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > attached base packages: > [1] stats graphics grDevices utils datasets methods base > other attached packages: > [1] arrayQualityMetrics_2.4.3 affyPLM_1.22.0 > [3] preprocessCore_1.8.0 gcrma_2.18.0 > [5] htmg430pmcdf_2.5.0 affy_1.24.2 > [7] Biobase_2.6.1 > loaded via a namespace (and not attached): > [1] affyio_1.14.0 annotate_1.24.0 AnnotationDbi_1.8.1 > [4] beadarray_1.14.0 Biostrings_2.14.8 DBI_0.2-4 > [7] genefilter_1.28.2 grid_2.10.1 hwriter_1.1 > [10] IRanges_1.4.9 lattice_0.17-26 latticeExtra_0.6-4 > [13] limma_3.2.1 marray_1.24.0 RColorBrewer_1.0-2 > [16] RSQLite_0.7-3 simpleaffy_2.22.0 splines_2.10.1 > [19] stats4_2.10.1 survival_2.35-8 tcltk_2.10.1 > [22] tools_2.10.1 vsn_3.14.0 xtable_1.5-6 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues
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