[BioC] Unable to read Affy Mouse Exon 1.0 ST array CEL file

[cstrato]

Dear Daisy,

You could try package "xps" which does not have memory limitations.

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
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On 8/10/11 8:37 PM, Dai, Hongying, wrote:
> Hi,
>
> I try to import CEL files generated from Affy Mouse Exon 1.0 ST array. I have tried both Affy and Oligo packages and my computer has 2.75GB RAM.
>
> *         Please let me know the following issue is package issue or computer RAM issue.
>
> *         Can any one share code to read  Affy Mouse Exon 1.0 ST array CEL files?
>
> Below is what I have tried so far. I have highlighted the error code and error message in red. All the other scripts ran well.
>
> I find pd.moex.1.0.st.v1 annotation package which provides Platform Design Info for Affymetrix MoEx-1_0-st-v1.
>
> First, I tried to import 12 CEL files using affy package:
>
>> library(affy)
>
>> library(pd.moex.1.0.st.v1)
>
>> a1<-ReadAffy()
>
> Error: cannot allocate vector of size 600.0 Mb
>
> In addition: Warning messages:
>
> 1: In read.affybatch(filenames = l$filenames, phenoData = l$phenoData,  :
>
>    Reached total allocation of 1535Mb: see help(memory.size)
>
> Secondly, I tried to import 1 CEL file using affy package each time and then combine these CEL files.
>
>> fns<- list.celfiles(full.names=TRUE)
>
>> temp1<-ReadAffy(filenames=fns[1])  #read 1 CEL, it works
>
>> temp2<-ReadAffy(filenames=fns[2])  #read another one CEL, it works
>
>> data<-merge.AffyBatch(temp1, temp2)
>
> Error: cannot allocate vector of size 100.0 Mb
>
> In addition: Warning messages:
>
> 1: In do.call(assayDataNew, c(list(exprs = exprs), dots)) :
>
> Reached total allocation of 1535Mb: see help(memory.size)
>
> Thirdly, I tried to perform gcrma analysis to 1 CEL.
>
>> lirary(gcrma)
>
>> eset1<- gcrma(temp1)
>
> Error in getCdfInfo(object) :
>
> Could not obtain CDF environment, problems encountered:
>
> Specified environment does not contain MoEx-1_0-st-v1
>
> Library - package moex10stv1cdf not installed
>
> Bioconductor - moex10stv1cdf not availableI then redo the code
>
> Fourthly, I tried to add in annotation file when reading 1 CEL file.
>
>> a1<-ReadAffy(filenames=fns[1],cdfname="pd.moex.1.0.st.v")
>
> Error: cannot allocate vector of size 50.0 Mb
>
> In addition: Warning messages:
>
> 1: In unlist(vlist, recursive = FALSE, use.names = FALSE) :
>
>    Reached total allocation of 1535Mb: see help(memory.size)
>
> After failure with appy package, I switched to oligo package to read 12 CEL files again.
>
>> library(oligo)
>
>> exonCELs<- list.celfiles(full.names = TRUE)
>
>> affyExonFS<- read.celfiles(exonCELs)
>
> Platform design info loaded.
>
> Error: cannot allocate vector of size 600.0 Mb
>
> In addition: Warning messages:
>
> 1: In smartReadCEL(filenames, sampleNames, headdetails = headdetails) :
>
> Reached total allocation of 1535Mb: see help(memory.size)
>
>
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>
> Daisy
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