Greetings, I have some samples measured by both U133A and U133B. Is there a way to combine results from these chips together into one result file? (i.e., take care of the replicated probe sets on both chips?) I took a look at the matchprobe package, but I think that is not exactly what I need. Thanks! Simon

The easiest way is to prefix each probeset ID with A or B indicating U133A and U133B. Suppose dataA and dataB represents your expression values from U133A and U133B respectively, then rownames(dataA) <- paste("A.", rownames(dataA), sep="") rownames(dataB) <- paste("B.", rownames(dataB), sep="") stopifnot( identical( colnames(dataA), colnames(dataB) ) ) newdata <- rbind( dataA, dataB ) write.table(newdata, file="output.txt", sep="\t", quote=FALSE) If you are thinking about calibrating U133A results to U133B, then the problem becomes more difficult. I asked a related question to this and you can search for the mailing list archives for the keywords "combining HGU133 chips". Regards, Adai. On Thu, 2004-07-15 at 17:41, Simon Lin wrote: > Greetings, > > I have some samples measured by both U133A and U133B. Is there a way to > combine results from these chips together into one result file? (i.e., take > care of the replicated probe sets on both chips?) > > I took a look at the matchprobe package, but I think that is not exactly > what I need. > > Thanks! > > Simon > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor >