[BioC] RMA error on exon arrays

[rcaloger]

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?

Cheers
Raffaele

-- 

----------------------------------------
Prof. Raffaele A. Calogero
Bioinformatics and Genomics Unit
Dipartimento di Scienze Cliniche e Biologiche
c/o Az. Ospedaliera S. Luigi
Regione Gonzole 10, Orbassano
10043 Torino
tel.   ++39 0116705417
Lab.   ++39 0116705408
Fax    ++39 0119038639
Mobile ++39 3333827080
email: raffaele.calogero at unito.it
       raffaele[dot]calogero[at]gmail[dot]com
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