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

Juan Pedro Steibel steibelj at msu.edu
Tue Oct 27 17:11:22 CET 2009

Please let me add one more possibility.

An alternative to filtering would be a "gene specific" (not probe 
specific) model that includes interaction of experimental effects (TRT) 
with probes, and test for such interaction gene-by-gene.
When you see a significant interaction of TRT by probe, you can manually 
align the sequences of the probes and see if they are hinting 
alternative splicing effects for example. If you do not see a 
significant interaction, just look at main effect of TRT.

I am not aware of a BioC package that can do this because this would 
imply different incidence matrices per gene (depending on number of 
replicated probes in each gene) and I have yet to find a package that 
can do it. But it is doable with "lmer" (lme4_lib) applied using the 
"by" function (both from R) for example (the moderated t-tests would be 
a challenge though).


Francois Pepin 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.
> 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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Juan Pedro Steibel

Assistant Professor
Statistical Genetics and Genomics

Department of Animal Science & 
Department of Fisheries and Wildlife

Michigan State University
1205-I Anthony Hall
East Lansing, MI
48824 USA 

Phone: 1-517-353-5102
E-mail: steibelj at msu.edu

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