[BioC] LIMMA - summarization of Illumina probes for same gene

Gordon K Smyth smyth at wehi.EDU.AU
Sun Mar 11 23:09:15 CET 2012

Dear Kripa,

Short answer:

If you really must average over multiple probes for a given gene, then the 
limma function you are looking for is avereps().

Longer answer:

This question has come up a few times recently on this mailing list, and I 
wonder whether you and other posters might be thinking of summarization as 
is done by the RMA algorithm for Affymetrix arrays over multiple probes 
in a probe-set.  The equivalent of this for an Illumina BeadChip is to 
summarize the multiple beads for each probe on each array.  This step is 
done by the Illumina Genome Studio software, so has already been completed 
before entry into limma.

On the other hand, summarizing multiple probes for a given gene (or 
multiple probe-sets for an Affy array) is not recommended as a routine 
procedure by any of the Bioconductor software developers.  The whole 
reason that multiple probes are provided by Illumina for a given gene is 
that the gene may take different isoforms to which the different probes 
may respond.  Why would you want to lose this information by pre-emptively 

Best wishes

> Date: Fri, 9 Mar 2012 21:42:58 +0000
> From: Kripa R <kripa777 at hotmail.com>
> To: <bioconductor at r-project.org>
> Subject: [BioC] LIMMA - summarization
> Hi everyone,

> I'm working on an analysis of illumina microarrays and am using the 
> limma package. But looking at the code provided with the vignette there 
> doesn't seem to be a summarization step (where multiple probes for the 
> same gene are combined)

> Am I missing something here or would I need to use a different package 
> to summarize (ie beadarray or lumi)?
> Thanks,
> -Kripa

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