[BioC] Create affyBatch from mouse exon array data using ReadAffy or extractAffyBatch() from aroma.affymetrix

[Henrik Bengtsson]

Hi,

I never received the original message for this one - was it posted to
BioC?  Anyway, my comments below.

On Wed, Jul 16, 2008 at 11:59 AM, cstrato <cstrato at aon.at> wrote:
> Dear An
>
> I cannot answer your question regarding aroma.affymetrix,
> but since you also mention "xps":
>
> Please note that xps can handle mouse exon arrays,
> see the file "script4xps.R" in directory examples of how
> to import the necessary clf, pgf and annotation files.
>
> Please let me know if you experience any problems.
>
> Best regards
> Christian
> _._._._._._._._._._._._._._._._
> C.h.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
> _._._._._._._._._._._._._._._._
>
> De Bondt, An-7114 [PRDBE] wrote:
>>
>> 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)

Actually, that is not doing anything but setting up the
AffymetrixCelSet.  It does not read in the data, except validating
that the CEL files are consistent with each other (and the CDF).  BTW,
you should only use 'checkChipType=FALSE', if you really know what you
are doing; if it gives an error otherwise, there is often a good
reason for it.

>>
>>
>> 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 see that you previously/below tried:

  affyBatchRaw <- extractAffyBatch(cs)

which is pretty much the same as the above.  In aroma.affymetrix we
use prefix "extract..." on method names to make it explicit that you
load all data into memory and that any changes done on the obtained
object will *not* be reflected in the underlying data files.

Having said all this, what you do above is not really utilizing the
aroma.affymetrix package at all.  All your problems are unrelated to
that package and has to do with the 'affy' package.

Your alternative is to do your exon analysis in 'aroma.affymetrix'
(see online Vignettes), or use 'xps' as Christian suggests.

Cheers

Henrik

>>
>> 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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>>
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