[BioC] microarray: dealing with multi probes for one gene

Francois Pepin fpepin at cs.mcgill.ca
Tue May 22 17:42:16 CEST 2007

Hi Christophe,

This is one of the classic questions on the list and I suggest that you
go through the archives
(http://dir.gmane.org/gmane.science.biology.informatics.conductor) for
more answers.

It depends on why you would have differences if the probes don't follow
the same profiles, as in Naomi's case, and which questions you are
trying to answer. For differential expression, you can often deal with
multiple probes per gene independently. If you are looking for gene set
enrichment (such as GO analyses), then the statistics expect a
measurement per gene.

As I said, the archives contain a lot of information on that particular


On Mon, 2007-05-21 at 10:19 +0200, Christophe Boutte wrote:
> Dear Bioconductors users,
> I make a post doc in the oceanic research station of Roscoff (France).
> I use the limma bioconductor for analysing microarray results.
> There is on my microarrays three replicates for each spot (thus I use 
> correlation or average to deal with these values).
> My problem is that we have several probes for each gene on the 
> microarray: we designed 1 to 5 different probes for each gene, and I do 
> not know how to use them:
> Should I average them ? It's difficult because the number of probes vary 
> depending of each gene (1-5) and I cannot precise the number of "dups". 
> I can also use correlation, but I have the same problem of variable 
> number of probes.
> Has somebody already dealt with this type of problem of variable 
> multi-probes by gene ?
> thank you in advance,
> Christophe Boutte
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