Question: DESeq2 design formula error?

0

Charles Determan Jr •

**140**wrote: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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modified 5.8 years ago
by
Steve Lianoglou ♦

**12k**• written 5.8 years ago by Charles Determan Jr •**140**