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

Francois Pepin fpepin at cs.mcgill.ca
Tue Oct 27 16:54:29 CET 2009

 > 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.

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.


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