[BioC] A few Q's on using DEXSeq with mucho data

[Steve Lianoglou]

Hi,

Imagine, if you will, that I have data for 7-8 different conditions
and I'd like to use DEXSeq to test for differential exon usage.

Is it best to create an ExonCountSet with all of my data (with an
appropriate design matrix that identifies which samples belong to
which condition) and do the estimateDispersion step with that?

My guess is yes, but I wanted to double check -- am I in danger of
maybe flagging some genes/exons as non-testable if, for example, it is
only expressed in 2 out of 8 conditions?

Assuming I should use all of my data to `estimateDisperion`s, what if
I only have one replicate for one of the 8 conditions, is it best to
remove it? I'm guessing it wouldn't provide any meaning information
for dispersion estimation since it's only one observation for that
condition.

Lastly, when testing for differences in exon usage, assuming I've been
using the data from all of my experiments up to this point, I don't
see a way to specify which experiments I want to specifically test.

If I run "the normal" DEXSeq analysis on my data, I end up with a
DEUresultTable that looks like it has log2fold(x/y) values for all
experiments against just one y. There is only one pvalue/padjust
column, so I'm not sure what comparison that is for.

Thanks for any help,
-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact