Search
Question: RMA error on exon arrays
0
gravatar for raffaele calogero
10.7 years ago by
Italy/Turin/University of Torino
raffaele calogero500 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.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
ADD COMMENTlink modified 10.7 years ago by James W. MacDonald45k • written 10.7 years ago by raffaele calogero500
0
gravatar for James W. MacDonald
10.7 years ago by
United States
James W. MacDonald45k wrote:
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.
ADD COMMENTlink written 10.7 years ago by James W. MacDonald45k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 160 users visited in the last hour