Greetings,

I have used the DESeq package previously and have been recently using
DESeq2.  I am particularly interested in repeated measures designs and was
wondering about applications with DESeq2.  I have read through the manual
and tried searching the archives but couldn't find too much direction for
testing over all timepoints instead of just one at a time (ANOVA-like
approach).  Reading the edgeR manual, it provides an example in section
3.3.4 that tests whether a treatment has an effect at any time by taking
multiple coefficients (i.e. lrt <- glmLRT(fit, coef=5:6)).  I attempted
something similar with DESeq2:

res <- results(dds, name=resultsNames(dds)[5:6]

but I got the warning message saying only the first element used:

Warning message:In if (paste0("WaldPvalue_", name) %in%
names(mcols(object))) { :
  the condition has length > 1 and only the first element will be used


Is there functionality with DESeq for looking over all timepoints or should
I stick to using edgeR for these types of experimental designs?  For
context, I prefer to use multiple techniques instead of just one for
further support given that no standard exists.

Many thanks,

-- 
Charles Determan
Integrated Biosciences PhD Candidate
University of Minnesota

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