
Dear UseRs,

I am analysing a dataset from mouse exon arrays using aroma.affymetrix.  I can read the raw data using following code.

      chipType <- "MmEx10stv1_Mm_ENSE"
      cdf <- AffymetrixCdfFile$fromChipType(chipType = chipType) 
      
      # setup the CEL set; read the raw data
      #==============
      projectName <- "myDataSet"
      cs <- AffymetrixCelSet$byName(projectName, chipType = chipType, checkChipType=FALSE, cdf = cdf) 



Next, I would like to make an AffyBatch from these raw data but I stumble at a memory message (see below).  This is the same message as directly
affyBatchRaw <- ReadAffy(filenames = paste("./rawData/myDataSet/MmEx10stv1_Mm_ENSE/", celfiles, sep = ""))

I am working on a linux machine with 70GB of memory.


Did anyone experience this before?  Is this typical for mouse exon arrays?  
I tried using exonmap as well as xps but, as far as I experienced, they are not yet adjusted for mouse exon arrays.

Thanks in advance for your help!

Kind regards,
An



>affyBatchRaw <- extractAffyBatch(cs)
Error in read.affybatch(filenames = l$filenames, phenoData = l$phenoData,  : 
        Calloc could not allocate (-1889533886 of 48) memory

> traceback()
5: .Call("read_abatch", filenames, rm.mask, rm.outliers, rm.extra, 
    ref.cdfName, dim.intensity, verbose, PACKAGE = "affyio")
4: read.affybatch(filenames = l$filenames, phenoData = l$phenoData, 
    description = l$description, notes = notes, compress = compress, 
    rm.mask = rm.mask, rm.outliers = rm.outliers, rm.extra = rm.extra, 
    verbose = verbose, sd = sd, cdfname = cdfname)
3: ReadAffy(filenames = filenames, sampleNames = sampleNames, ..., 
    verbose = as.logical(verbose))
2: extractAffyBatch.AffymetrixCelSet(cs)
1: extractAffyBatch(cs)

>sessionInfo()
R version 2.6.2 (2008-02-08) 
x86_64-unknown-linux-gnu 

locale:
    LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
    [1] tools     stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
    [1] mmex10stv1mmensecdf_10.0.0 farms_1.3.1               
[3] MASS_7.2-42                preprocessCore_1.0.0      
[5] affyio_1.6.1               Biobase_1.16.3            
[7] aroma.affymetrix_0.9.3     aroma.apd_0.1.3           
[9] R.huge_0.1.5               affy_1.16.0               
[11] affxparser_1.10.2          aroma.core_0.9.3          
[13] sfit_0.1.5                 aroma.light_1.8.1         
[15] digest_0.3.1               matrixStats_0.1.2         
[17] R.rsp_0.3.4                R.cache_0.1.7             
[19] R.utils_1.0.2              R.oo_1.4.3                
[21] R.methodsS3_1.0.1         

loaded via a namespace (and not attached):
    [1] rcompgen_0.1-17




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