[Bioc-devel] [BioC] error with AffyQCReport
Wolfgang Huber
huber at ebi.ac.uk
Fri Feb 9 14:37:21 CET 2007
Dear Mark,
I don't have the input data that you used to get your error, and I
couldn't reproduce it by running the script
affyQCReport/inst/scripts/DilutionExample.R which is in the package.
It looks though as if it has to do with the way that your affy.object is
constructed. The call to "boxplot" is not dispatched to the AffyBatch
method "boxplot" but rather to "boxplot.default".
Mark, could you post your input data so others can reproduce your
problem and try to figure out what is going. You could also check
yourself by going into this level of the call stack:
2: signalDist(object)
and see what class "object" is and why it then calls the wrong boxplot
method.
Best wishes
Wolfgang
> 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"
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