[BioC] Methods to combine U133A and B?

Adaikalavan Ramasamy ramasamy at cancer.org.uk
Thu Jul 15 20:11:04 CEST 2004

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
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