install.packages("ff")

library(ff)

then run

library(oligo)
exonCELs <- list.celfiles(full.names = TRUE)

and so on

it might help you get through this with smaller consumption


On Wed, Aug 10, 2011 at 2:37 PM, Dai, Hongying, <hdai@cmh.edu> 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)
>
>
>
>
> Daisy
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
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