[BioC] Error in function read.spikein of affycomp

[cstrato]

Dear Benilton

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).

Best regards
Christian

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,
>
> b
>
> 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"),
>>                         remove.xhyb=TRUE){
>>  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
>>  if(cdfName=="hgu95a"){
>>    data(spikein.phenodata)
>>    pd <- spikein.phenodata
>>  }
>>  if(cdfName=="hgu133a"){
>>    data(hgu133a.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)
>>  return(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
>> Christian
>>
>>
>> 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 
>>> data:
>>>
>>>> s <- read.spikein("s_RMA.csv")
>>> Error in function (classes, fdef, mtable)  :
>>> unable to find an inherited method for function "pData", for
>>> signature "phenoData"
>>>
>>>> sessionInfo()
>>> R version 2.8.0 (2008-10-20)
>>> i386-apple-darwin8.11.1
>>>
>>> locale:
>>> C
>>>
>>> attached base packages:
>>> [1] tools     stats     graphics  grDevices utils     datasets
>>> methods  [8] base
>>> other attached packages:
>>> [1] affycomp_1.18.0 Biobase_2.2.1  >
>>>
>>> Do you know the reason for this error?
>>>
>>> Best regards
>>> Christian
>>> _._._._._._._._._._._._._._._._._._
>>> 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
>>> _._._._._._._._._._._._._._._._._._
>>>
>>> _______________________________________________
>>> Bioconductor mailing list
>>> Bioconductor at stat.math.ethz.ch
>>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>>> Search the archives:
>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>
>>>
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at stat.math.ethz.ch
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives: 
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>