Question: DESeq2 design formula error?
5.9 years ago by
Charles Determan Jr • 140
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.  "(Intercept)" "subject.2"  "subject.3" "subject.4"  "subject.5" "group.Treated"  "group.Control:times1 "group.Treated:times1"  "group.Control:times2 "group.Treated:times2"  "group.Control:times3 "group.Treated:times3" Thanks for any insight, -- Charles Determan Integrated Biosciences PhD Candidate University of Minnesota [[alternative HTML version deleted]]
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