[BioC] error with AffyQCReport
Mark W Kimpel
mwkimpel at gmail.com
Tue Feb 6 01:29:43 CET 2007
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]
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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