Hi Andreas,

Use the annotation db for your chip (e.g. hgu133aENSEMBL,
hgu133aREFSEQ, hgu133aSYMBOL, hgu133aUNIGENE) to get a grouping variable:

> map.x <- unlist(as.list(hgu133aUNIGENE))
> head(map.x)
  1007_s_at     1053_at      117_at      121_at   1255_g_at     1294_at
"Hs.631988" "Hs.647062" "Hs.654614" "Hs.469728"  "Hs.92858"  "Hs.16695"

you can use something like:

collapsed.m <- by(mydata, map.x, median)

or if you want the mean
limma::avereps



Regards,
Amos Folarin


---------- Forwarded message ----------
From: Mete Civelek <mcivelek@mednet.ucla.edu>
To: <bioconductor@r-project.org>
Date: Thu, 28 Apr 2011 10:18:09 -0700
Subject: Re: [BioC] collapsing redundant probe sets of Affymetrix Chips
Hi Andreas,

Try the function avereps in limma.

Mete

-----Original Message-----
From: bioconductor-bounces@r-project.org
[mailto:bioconductor-bounces@r-project.org] On Behalf Of Andreas Heider
Sent: Thursday, April 28, 2011 2:13 AM
To: bioconductor@r-project.org
Subject: [BioC] collapsing redundant probe sets of Affymetrix Chips

Hi bioconductor mailing list,
I got a (another) problem with redundant probesets from Affymetrix chips:
For my downstream analysis to work, I need only 1 expression value per gene
(eg Entrez Id).
So by now I have a table that looks something like this:

 N probe set gene id expression  1 *12345_at* *123* 1.5  2 123456_at 1234 2
3 *1234567_at* *123* 1.6  4 12345678_at 12345 4  5 *123456789_at* *123* 1.4
By collapsing I mean as a result something like this:

 N probe set gene id expression
 1 *12345_at* *123* *1.5* <= eg median  2 123456_at 1234 2
 4 12345678_at 12345 4

I hope one can help me out! I have seen this in several publications, so
there must be a way.

Thanks in advance, Andreas Heider

       [[alternative HTML version deleted]]

	[[alternative HTML version deleted]]

