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De Bondt, An-7114 [PRDBE]
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@de-bondt-an-7114-prdbe-1572
Last seen 10.3 years ago
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=e
n_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.U
TF-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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