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

[cstrato]

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) 
>
>
>
> 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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