[BioC] collapsing redundant probe sets of Affymetrix Chips

[Mete Civelek]

Hi Andreas,

Try the function avereps in limma.

Mete

-----Original Message-----
From: bioconductor-bounces at r-project.org
[mailto:bioconductor-bounces at r-project.org] On Behalf Of Andreas Heider
Sent: Thursday, April 28, 2011 2:13 AM
To: bioconductor at 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]]

_______________________________________________
Bioconductor mailing list
Bioconductor at r-project.org
https://stat.ethz.ch/mailman/listinfo/bioconductor
Search the archives:
http://news.gmane.org/gmane.science.biology.informatics.conductor


IMPORTANT WARNING:  This email (and any attachments) is ...{{dropped:9}}