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.z ip) 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 www: www.bioinformatica.unito.it

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.ta r.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 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.