Jim, Nope, I don't think that's it. I have 29 CEL files. I also looked at nchar instead of length. Here's the output: affy.object<-ReadAffy(phenoData = adf) > paste(experiment.designator, "AffyQCReport.pdf", sep=".") [1] "RL02.AffyQCReport.pdf" > length(paste(experiment.designator, "AffyQCReport.pdf", sep=".")) [1] 1 > nchar(paste(experiment.designator, "AffyQCReport.pdf", sep=".")) [1] 21 > length(list.celfiles()) [1] 29 > James W. MacDonald wrote: > Hi Mark, > > Mark W Kimpel wrote: >> Wolfgang, >> >> I installed a fresh build of R 2.5.0-devel 2 days ago and updated all >> my devel packages today. I get the same error. See my debugging >> output below. Note that read.AnnotatedDataFrame.ordered is my own >> function to keep me from accidentally not ordering my text file in >> the same order as my cel.files. The last I knew read.phenoData did >> not include this feature and I really screwed up an analysis because >> of it. Anyway, my function code it immediately below. I'm copying to >> BioC-devel list as that might be the best place to continue this. >> >> Thanks, >> Mark >> >> #reads in unsorted phenodata type file and makes and adf. "adf.txt" >> MUST have celfiles names without ".CEL" as sample names in first column >> ################################################################### ##### >> read.AnnotatedDataFrame.ordered.func<-function(adf.file="adf.txt") >> { >> require(affy, quiet=TRUE) >> adf<-read.AnnotatedDataFrame(adf.file, header=TRUE, sep="\t", >> row.names=1) >> cel.files<-list.celfiles() >> pos<-pmatch(rownames(pData(adf)), cel.files) >> adf<-adf[pos,] >> adf >> } >> ############################################################ >> #Session output >> > #QC >> > adf<-read.AnnotatedDataFrame.ordered.func() >> > >> > affy.object<-ReadAffy(phenoData=adf) >> > >> > QCReport(object=affy.object,file=paste(experiment.designator, >> "AffyQCReport.pdf", sep=".")) >> Error in attr(groups, "names") <- names : 'names' attribute [29] must >> be the same length as the vector [1] > > What exactly is 'experiment.designator'? I can get this function to > work (although I get a different warning I am trying to track down). > What do you get when you do > > paste(experiment.designator, "AffyQCReport.pdf", sep=".") > > at an R prompt? From the error I am betting you get something of > length 29. > > Best, > > Jim > > >> >> Enter a frame number, or 0 to exit >> >> 1: QCReport(object = affy.object, file = paste(experiment.designator, >> "AffyQCReport.pdf", sep = ".")) >> 2: signalDist(object) >> 3: boxplot(object, names = ArrayIndex, ylab = "Log2(Intesity)", xlab >> = "Array Index") >> 4: boxplot.default(object, names = ArrayIndex, ylab = >> "Log2(Intesity)", xlab = "Array Index") >> >> Selection: 4 >> Called from: eval(expr, envir, enclos) >> Browse[1]> ls() >> [1] "*tmp*" "add" "args" "at" "border" "col" "groups" "horizontal" >> "log" "n" "namedargs" >> [12] "names" "notch" "outline" "pars" "plot" "range" "varwidth" >> "width" "x" >> Browse[1]> names >> [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" "14" "15" >> "16" "17" "18" "19" "20" "21" "22" "23" "24" "25" "26" "27" "28" "29" >> Browse[1]> groups >> [[1]] >> AffyBatch object >> size of arrays=834x834 features (182056 kb) >> cdf=Rat230_2 (31099 affyids) >> number of samples=29 >> number of genes=695556 >> annotation=rat2302 >> notes= >> >> Browse[1]> c >> >> Enter a frame number, or 0 to exit >> >> 1: QCReport(object = affy.object, file = paste(experiment.designator, >> "AffyQCReport.pdf", sep = ".")) >> 2: signalDist(object) >> 3: boxplot(object, names = ArrayIndex, ylab = "Log2(Intesity)", xlab >> = "Array Index") >> 4: boxplot.default(object, names = ArrayIndex, ylab = >> "Log2(Intesity)", xlab = "Array Index") >> >> Selection: 0 >> > sessionInfo() >> R version 2.5.0 Under development (unstable) (2007-01-31 r40628) >> i386-pc-mingw32 >> >> locale: >> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >> States.1252;LC_MONETARY=English_United >> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] "splines" "stats" "graphics" "grDevices" "datasets" "utils" >> "tools" "methods" "base" >> >> other attached packages: >> rat2302cdf affyQCReport lattice geneplotter RColorBrewer affyPLM >> gcrma matchprobes affydata xtable simpleaffy >> "1.15.0" "1.13.16" "0.14-16" "1.12.0" "0.2-3" "1.11.13" "2.7.1" >> "1.7.4" "1.11.1" "1.4-3" "2.9.1" >> affycoretools biomaRt RCurl XML GOstats Category genefilter survival >> KEGG RBGL annotate >> "1.6.0" "1.6.3" "0.8-0" "1.4-1" "2.1.11" "2.1.11" "1.13.8" "2.31" >> "1.15.1" "1.11.4" "1.13.6" >> GO graph limma affy affyio Biobase >> "1.15.1" "1.13.5" "2.9.9" "1.13.14" "1.3.3" "1.13.34" >> >> Wolfgang Huber wrote: >> >>> Dear Mark, >>> >>> the parts of Biobase and of the affyQCReport packages that may be >>> involved in your problem have changed quite a lot since the 1.9 >>> release. >>> Would you mind trying to see whether you get the same (or another) >>> problem with a current R-devel and the devel versions of the packages? >>> Otherwise we may end up chasing bugs that are long gone... >>> >>> Best wishes >>> Wolfgang >>> >>> >>> >>> W Kimpel wrote: >>> >>> >>>> I am getting an error with QCReport of package affyQCReport. >>>> Debugging info and sessionInfo() follows. It looks to me like the >>>> group attributes is not being extracted properly from the >>>> affyObject. SampleNames that match the CEL files are stored in the >>>> first column of Data. >>>> >>>> I am using the current version of R and BioC packages, not the >>>> devel versions. >>>> >>>> Thanks, >>>> Mark >>>> >>>> >>>> > ?QCReport >>>> > paste(experiment.designator, "AffyQCReport.pdf", sep=".") >>>> [1] "RL02.AffyQCReport.pdf" >>>> > QCReport(object=affy.object,file=paste(experiment.designator, >>>> "AffyQCReport.pdf", sep=".")) >>>> Error in attr(groups, "names") <- names : 'names' attribute [29] >>>> must be the same length as the vector [1] >>>> >>>> Enter a frame number, or 0 to exit >>>> 1: QCReport(object = affy.object, file = >>>> paste(experiment.designator, "AffyQCReport.pdf", sep = ".")) >>>> 2: signalDist(object) >>>> 3: boxplot(object, names = ArrayIndex, ylab = "Log2(Intesity)", >>>> xlab = "Array Index") >>>> 4: boxplot.default(object, names = ArrayIndex, ylab = >>>> "Log2(Intesity)", xlab = "Array Index") >>>> >>>> Selection: 2 >>>> Called from: eval(expr, envir, enclos) >>>> Browse[1]> ls() >>>> [1] "ArrayIndex" "object" Browse[1]> ArrayIndex >>>> [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" >>>> "13" "14" "15" "16" "17" "18" "19" "20" "21" "22" "23" "24" "25" >>>> "26" "27" "28" "29" >>>> Browse[1]> object >>>> AffyBatch object >>>> size of arrays=834x834 features (157603 kb) >>>> cdf=Rat230_2 (31099 affyids) >>>> number of samples=29 >>>> number of genes=31099 >>>> annotation=rat2302 >>>> Browse[1]> c >>>> >>>> Enter a frame number, or 0 to exit >>>> 1: QCReport(object = affy.object, file = >>>> paste(experiment.designator, "AffyQCReport.pdf", sep = ".")) >>>> 2: signalDist(object) >>>> 3: boxplot(object, names = ArrayIndex, ylab = "Log2(Intesity)", >>>> xlab = "Array Index") >>>> 4: boxplot.default(object, names = ArrayIndex, ylab = >>>> "Log2(Intesity)", xlab = "Array Index") >>>> >>>> Selection: 3 >>>> Called from: eval(expr, envir, enclos) >>>> Browse[1]> boxplot >>>> function (x, ...) >>>> UseMethod("boxplot") >>>> <environment: namespace:graphics=""> >>>> Browse[1]> ls() >>>> [1] "x" >>>> Browse[1]> x >>>> AffyBatch object >>>> size of arrays=834x834 features (157603 kb) >>>> cdf=Rat230_2 (31099 affyids) >>>> number of samples=29 >>>> number of genes=31099 >>>> annotation=rat2302 >>>> Browse[1]> c >>>> >>>> Enter a frame number, or 0 to exit >>>> 1: QCReport(object = affy.object, file = >>>> paste(experiment.designator, "AffyQCReport.pdf", sep = ".")) >>>> 2: signalDist(object) >>>> 3: boxplot(object, names = ArrayIndex, ylab = "Log2(Intesity)", >>>> xlab = "Array Index") >>>> 4: boxplot.default(object, names = ArrayIndex, ylab = >>>> "Log2(Intesity)", xlab = "Array Index") >>>> >>>> Selection: 4 >>>> Called from: eval(expr, envir, enclos) >>>> Browse[1]> ls() >>>> [1] "*tmp*" "add" "args" "at" >>>> "border" "col" "groups" "horizontal" "log" >>>> "n" "namedargs" >>>> [12] "names" "notch" "outline" "pars" >>>> "plot" "range" "varwidth" "width" "x" >>>> Browse[1]> dim(x) >>>> NULL >>>> Browse[1]> names >>>> [1] "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" >>>> "13" "14" "15" "16" "17" "18" "19" "20" "21" "22" "23" "24" "25" >>>> "26" "27" "28" "29" >>>> Browse[1]> attr(groups,names) >>>> Error during wrapup: exactly one attribute 'name' must be given >>>> Browse[1]> groups >>>> [[1]] >>>> AffyBatch object >>>> size of arrays=834x834 features (157603 kb) >>>> cdf=Rat230_2 (31099 affyids) >>>> number of samples=29 >>>> number of genes=31099 >>>> annotation=rat2302 >>>> >>>> Browse[1]> c >>>> >>>> Enter a frame number, or 0 to exit >>>> 1: QCReport(object = affy.object, file = >>>> paste(experiment.designator, "AffyQCReport.pdf", sep = ".")) >>>> 2: signalDist(object) >>>> 3: boxplot(object, names = ArrayIndex, ylab = "Log2(Intesity)", >>>> xlab = "Array Index") >>>> 4: boxplot.default(object, names = ArrayIndex, ylab = >>>> "Log2(Intesity)", xlab = "Array Index") >>>> >>>> Selection: 0 >>>> > sessionInfo() >>>> R version 2.4.1 (2006-12-18) >>>> i386-pc-mingw32 >>>> >>>> locale: >>>> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United >>>> States.1252;LC_MONETARY=English_United >>>> States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 >>>> >>>> attached base packages: >>>> [1] "splines" "stats" "graphics" "grDevices" "datasets" >>>> "utils" "tools" "methods" "base" >>>> other attached packages: >>>> rat2302cdf affyQCReport simpleaffy affycoretools >>>> biomaRt RCurl XML GOstats Category >>>> genefilter survival >>>> "1.14.0" "1.12.0" "2.8.0" "1.6.0" >>>> "1.8.1" "0.8-0" "1.2-0" "2.0.4" >>>> "2.0.3" "1.12.0" "2.30" >>>> KEGG RBGL annotate GO >>>> graph RWinEdt limma affy affyio >>>> Biobase >>>> "1.14.1" "1.10.0" "1.12.1" "1.14.1" >>>> "1.12.0" "1.7-5" "2.9.1" "1.12.2" >>>> "1.2.0" "1.12.2" >>>> >>>> >>> >>> >>> >> >> > > -- Mark W. Kimpel MD Neuroinformatics Department of Psychiatry Indiana University School of Medicine