[BioC] RMA error on exon arrays

[James W. MacDonald]

Hi Raffaele,

rcaloger wrote:
> Hi,
> I am trying to calculate probe sets summary on a test set of exon arrays 
> from Affymetrix data set (3 breast vs 3 cerebellum, 
> http://www.bioinformatica.unito.it/bioinformatics/DAGEL.II/exon.data.zip) 
> using a compiled cdf file for linux 
> (http://www.bioinformatica.unito.it/downloads/huex10stv2cdf_1.0.0.tar.gz).
> I get an error if I use rma or expresso.
> The error is associated to the normalization procedure (quantile).
>  >tmp
> AffyBatch object
> size of arrays=2560X2560 (307212 kb)
> cdf=HuEx-1_0-st-v2 (1432154 affyids)
> number of samples=6
> number of genes=1432154
> annotation=huex10stv2
> debug (rma)
> tmp.rma <- rma(tmp)
> error of Error in FUN(X[[1411190L]], ...): subscript out of bounds
> the error comes during this call
> exprs <- .Call("rma_c_complete", pm(object, subset), mm(object, subset), 
> probeNames(object, subset), ngenes, body(bg.dens),
> new.env(), normalize, background, bgversion, PACKAGE="affy")
> 
> same error cames during the normalization process  if I use expresso:
> tmp.rma <- expresso(tmp, bgcorrect.method="rma",
>                      normalize.method="quantile", pmcorrect.method="pmonly",
>                      summary.method="median.polish")
> 
> My system is SUN 2 X dual-core AMD Opteron processor 2218, 24 Gb RAM running SUSE Linux Enterprise Server 10
> Bioconductor 1.9
> 
> Any suggestion how to solve the problem?

I haven't used the cdf package you are using, but have had success with 
the ones you can get here:

http://xmap.picr.man.ac.uk/download/index.jsp

Best,

Jim


> 
> Cheers
> Raffaele
> 


-- 
James W. MacDonald
Affymetrix and cDNA Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
734-647-5623


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