[BioC] [Bioc-devel] error with AffyQCReport
James W. MacDonald
jmacdon at med.umich.edu
Tue Feb 6 23:10:20 CET 2007
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"
>>>
>>>
>>
>>
>>
>
>
--
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623
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