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

[Massimo Pinto]

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.

Francois
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 :
http://www.bioconductor.org/workshops/2006/BioC2006/labs/rgentleman/GSEA.pdf
thank you
Massimo
>
> 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
>