[BioC] Agi4x44PreProcess 1.4.0 question: use of genes.rpt.agi() and Gene Sets

Massimo Pinto pintarello at gmail.com
Thu Oct 29 00:01:45 CET 2009

On Tue, Oct 27, 2009 at 4:54 PM, Francois Pepin <fpepin at cs.mcgill.ca> wrote:
>> Are there any functions written to address each of these topics?
>> 1) choosing the probe with the largest experimental variation (or with
>> the maximum average)
> ?genefilter::findLargest should point you in the right direction.

Looks like this is the one. These issues are discussed in Gene Set
Enrichment Analysis, such as in this document from a 2006 BioC
workshop :
thank you
> I've found interquartile range (?IQR) works well in many cases in addition
> to variance. I'm not convinced maximum average is ideal, but I've never
> tried it.
>> 2) choosing the probe that maps closest to the 3' end
> I have yet to find a good solution for this. We've blasted all probes on the
> genome, but the poly-A isn't always easy to get in an automated way. Maybe
> someone else found a nicer way to get it done.
> My strategy is to use strategy 1) for most of the analysis and then check
> the distance to 3' manually for the genes of interest. We are doing 2 rounds
> of amplification and tend to have short fragments, so checking the 3' end is
> necessary.
> Francois

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