[BioC] Error in function read.spikein of affycomp
cstrato at aon.at
Tue Dec 16 19:57:59 CET 2008
Thank you for this information, using affycomp_1.19.3 solved my problem.
I have tested that it works with R 2.8.0, however I had to change the
Depends field of DESCRIPTION to R (>=R.2.8.0), Biobase (>=2.2.1).
Benilton Carvalho wrote:
> I'm not in position to give it a try now, but have you tried affycomp
> in BioC-devel???
> I did fix something similar to this there not long ago.
> Thank you,
> On Dec 15, 2008, at 7:52 PM, cstrato wrote:
>> Dear Rafael
>> Meanwhile I looked at the source code of "affycomp" and realized that it
>> contains defunct Biobase classes.
>> When changing the code for function "read.spikein" to:
>> read.spikein <- function(filename,cdfName=c("hgu95a","hgu133a"),
>> cdfName <- match.arg(cdfName)
>> s <- read.csv(filename,check.names=FALSE,row.names=1)
>> samplenames <- colnames(s)
>> ##remove the .cel if its there
>> samplenames <- sub("\\.gz$","",samplenames,ignore.case=TRUE)
>> samplenames <- sub("\\.Z$","",samplenames,ignore.case=TRUE)
>> samplenames <- sub("\\.cel$","",samplenames,ignore.case=TRUE)
>> colnames(s) <- samplenames
>> ##read phenodata
>> pd <- spikein.phenodata
>> pd <- hgu133a.spikein.phenodata
>> pd <- as(pd,"AnnotatedDataFrame") #<== new
>> ##putit in order
>> s <- s[,rownames(pData(pd))]
>> s <- log(s) #<== new
>> s <- new("ExpressionSet",exprs=as.matrix(s),phenoData=pd)
>> #delete s <- exprset.log(s) ##take log
>> if(remove.xhyb & cdfName=="hgu133a") s <- remove.hgu133a.xhyb(s)
>> then I can import the example using:
>>> s <- read.spikein.test("s_rma.csv")
>> However, then I get the next error:
>>> assess.rma <- assessSpikeIn(s, method.name="RMA")
>> Performing 6 assessments that will take a few minutes.....Error:
>> 'geneNames' is defunct.
>> Use 'featureNames' instead.
>> See help("Defunct") and help("Biobase-defunct").
>> It would be great if you could update the "affycomp" package asap to
>> work with BioC 2.3.
>> Thank you in advance.
>> Best regards
>> cstrato wrote:
>>> Dear all,
>>> I would like to use affycomp for my data, but even using the example
>>> data "s_RMA.csv" I get the following error when trying to read the
>>>> s <- read.spikein("s_RMA.csv")
>>> Error in function (classes, fdef, mtable) :
>>> unable to find an inherited method for function "pData", for
>>> signature "phenoData"
>>> R version 2.8.0 (2008-10-20)
>>> attached base packages:
>>>  tools stats graphics grDevices utils datasets
>>> methods  base
>>> other attached packages:
>>>  affycomp_1.18.0 Biobase_2.2.1 >
>>> Do you know the reason for this error?
>>> Best regards
>>> C.h.r.i.s.t.i.a.n S.t.r.a.t.o.w.a
>>> V.i.e.n.n.a A.u.s.t.r.i.a
>>> e.m.a.i.l: cstrato at aon.at
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>>> Bioconductor at stat.math.ethz.ch
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