Dear R-Help, I am trying to use affycomp to do some assessments of a new method with the spikein data using the Hgu-133 chip. Just to make sure that the problem was in affycomp in not in my method, I used the affy package version of RMA to do create the CSV file. Here's what I did: > spike133 <- ReadAffy() > spike133 AffyBatch object size of arrays=712x712 features (166358 kb) cdf=HG-U133A_tag (22300 affyids) number of samples=42 number of genes=22300 annotation=hgu133atag > bgcrma <- expresso(spike133,bgcorrect.method="rma",normalize.method= "quantiles",pmcorrect.method="pmonly",summary.method="medianpolish") background correction: rma normalization: quantiles PM/MM correction : pmonly expression values: medianpolish background correcting...done. normalizing...done. 22300 ids to be processed ## Transform back to original scale, as per directions on Affycomp website: > eset <- exprs(bgcrma) > log.bgcrma <- bgcrma > exprs(bgcrma) <- 2^eset > new.eset <- exprs(bgcrma) > write.table(data.frame(new.eset,check.names=FALSE),"rma-133.csv",sep =",",col.names=NA,quote=FALSE) > library(affycomp) > read.spikein("rma-133.csv") Error in "[.data.frame"(s, , rownames(pData(pd))) : undefined columns selected The funny thing is that when I follow the same procedures with the spikein data on the HGU-95 chip, I have no problem reading the data into affycomp. FYI - Here the version of R I am using: R : Copyright 2005, The R Foundation for Statistical Computing Version 2.2.0 (2005-10-06 r35749) ISBN 3-900051-07-0 I am running R on Mac OS X (Tiger) using R-Aqua 2.2.1, r-app 1.13. I had a student run the same scenario on a PC and he received the same result. Thank you for your help, Monnie Monnie McGee, Ph.D. Assistant Professor Department of Statistical Science Southern Methodist University Ph: 214-768-2462 Fax: 214-768-4035

Dear R-Help, If I had read the affycomp vignette a little more closely, I could have answered this question without sending an e-mail to the list. However, in case you are wondering, the function "read.newspikein" works with the HGU-133 SpikeIn data. The function "read.spikein" is for the HGU-95 SpikeIn data. Cheers, Monnie Monnie McGee, Ph.D. Assistant Professor Department of Statistical Science Southern Methodist University Ph: 214-768-2462 Fax: 214-768-4035 -----Original Message----- From: McGee, Monnie Sent: Sun 12/18/2005 8:55 PM To: bioconductor at stat.math.ethz.ch Subject: Data Frame Error in Affycomp Dear R-Help, I am trying to use affycomp to do some assessments of a new method with the spikein data using the Hgu-133 chip. Just to make sure that the problem was in affycomp in not in my method, I used the affy package version of RMA to do create the CSV file. Here's what I did: > spike133 <- ReadAffy() > spike133 AffyBatch object size of arrays=712x712 features (166358 kb) cdf=HG-U133A_tag (22300 affyids) number of samples=42 number of genes=22300 annotation=hgu133atag > bgcrma <- expresso(spike133,bgcorrect.method="rma",normalize.method= "quantiles",pmcorrect.method="pmonly",summary.method="medianpolish") background correction: rma normalization: quantiles PM/MM correction : pmonly expression values: medianpolish background correcting...done. normalizing...done. 22300 ids to be processed ## Transform back to original scale, as per directions on Affycomp website: > eset <- exprs(bgcrma) > log.bgcrma <- bgcrma > exprs(bgcrma) <- 2^eset > new.eset <- exprs(bgcrma) > write.table(data.frame(new.eset,check.names=FALSE),"rma-133.csv",sep =",",col.names=NA,quote=FALSE) > library(affycomp) > read.spikein("rma-133.csv") Error in "[.data.frame"(s, , rownames(pData(pd))) : undefined columns selected The funny thing is that when I follow the same procedures with the spikein data on the HGU-95 chip, I have no problem reading the data into affycomp. FYI - Here the version of R I am using: R : Copyright 2005, The R Foundation for Statistical Computing Version 2.2.0 (2005-10-06 r35749) ISBN 3-900051-07-0 I am running R on Mac OS X (Tiger) using R-Aqua 2.2.1, r-app 1.13. I had a student run the same scenario on a PC and he received the same result. Thank you for your help, Monnie Monnie McGee, Ph.D. Assistant Professor Department of Statistical Science Southern Methodist University Ph: 214-768-2462 Fax: 214-768-4035