[BioC] [Bioc-devel] error with AffyQCReport
Mark W Kimpel
mwkimpel at gmail.com
Wed Feb 7 06:39:02 CET 2007
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
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