AH. GS==GeneSpring. If you want to join them before importing to GeneSpring, you should do this after computing expression values. You can do something like: out <- rbind(exprs(exprSetA), exprs(exprSetB)) write.table(out, "Combined expression data.txt", sep="\t", quote=F, col.names=NA) HTH, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> "Lizhe Xu" <lxu@chnola-research.org> 03/14/04 06:20PM >>> Now, I tried to load the exported data from Bioconductor to GeneSpring and found another question. Since I used U133 chip set, I wonder if I can joint the U133A and B directly and import them to GS or I should do probeset level normalization first (if so, which package in bioconductor can do it) before joint them. Thanks. Lxu _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

The rownames of HGU-133A and HGU-133B are not unique (there is about 100+ redundancies). You might want to add these codes before rbind() to avoid any confusion later. A <- exprs(exprSetA) rownames(A) <- paste("A.", rownames(A)) B <- exprs(exprSetB) rownames(B) <- paste("B.", rownames(B)) Also, doing normalization before summary is better because we have more information to utilize at probe level. > -----Original Message----- > From: bioconductor-bounces@stat.math.ethz.ch > [mailto:bioconductor-bounces@stat.math.ethz.ch]On Behalf Of James > MacDonald > Sent: 15 March 2004 14:11 > To: lxu@chnola-research.org; bioconductor@stat.math.ethz.ch > Subject: Re: [BioC] questions about Affy package from new user: onemore > question > > > AH. GS==GeneSpring. > > If you want to join them before importing to GeneSpring, you should do > this after computing expression values. You can do something like: > > out <- rbind(exprs(exprSetA), exprs(exprSetB)) > write.table(out, "Combined expression data.txt", sep="\t", quote=F, > col.names=NA) > > HTH, > > Jim > > > > James W. MacDonald > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > >>> "Lizhe Xu" <lxu@chnola-research.org> 03/14/04 06:20PM >>> > Now, I tried to load the exported data from Bioconductor to GeneSpring > and found another question. Since I used U133 chip set, I wonder if I > can joint the U133A and B directly and import them to GS or I should do > probeset level normalization first (if so, which package in bioconductor > can do it) before joint them. Thanks. > > Lxu > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >