Hello,
I am trying to use DESeq to test for differential expression in a
multi-factor, multi-condition experiment. Factor 1 (Blocking) has 2
conditions, Factor 2 (Time) has 4 conditions and Factor 3 (exposure) has 2
conditions.

I am interested in making pairwise comparisons between time points while
utilizing a model containing Blocking and Exposure parameters:

fit1 <- nbinomFitGLM(cds, count ~ Blocking + Exposure )
fit2 <- nbinomFitGLM(cds, count ~ Blocking + Exposure + Time)
pvals <- nbinomGLMTest( fit2, fit1 )

I am unclear whether the significant genes returned by this analysis are
significant across all time points or any time point. Is there a way to
test pairwise (time1 vs. time2) while preserving the blocking and exposure
components (ie not using nbinomTest to directly compare time1 and time 2)

Thanks for the help!
Andrew

-- 
Andrew Lysaght
Cyclocross Captain, MIT Cycling
Ph.D. Candidate
Program in Speech and Hearing Bioscience and Technology
Harvard/MIT Division of Health Sciences and Technology

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