Entering edit mode
Amos Folarin
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80
@amos-folarin-4200
Last seen 10.1 years ago
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
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