Greetings,

I am trying to run an interaction formula with DESeq2.  I try and run the
following code and get the following error:

> design(DESeq.cds) <- formula(~ subject+group+group:times)> DESeq.cds <- DESeq(DESeq.cds)estimating size factorsestimating dispersionsyou had estimated dispersions, replacing thesegene-wise dispersion estimatesError in modelMatrixNames[match(convertNames$from, modelMatrixNames)] <- convertNames$to :
  NAs are not allowed in subscripted assignments


I am not sure exactly what this means.  I have uneven groups sizes but it
doesn't seem to be an issue when I have the design:

> design(DESeq.cds) <- formula(~ subject+times+group+group:times)


But the above formula doesn't provide the contrasts I would like.  I would
like to have the coefficients to be as follows so I can report how the
genes change in response in the different groups over time.

 [1] "(Intercept)"             "subject.2"
 [3] "subject.3"               "subject.4"
 [5] "subject.5"               "group.Treated"
 [7] "group.Control:times1 "group.Treated:times1"
 [9] "group.Control:times2 "group.Treated:times2"
[11] "group.Control:times3 "group.Treated:times3"


Thanks for any insight,

-- 
Charles Determan
Integrated Biosciences PhD Candidate
University of Minnesota

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