DESeq and checkFullRank(modelMatrix)
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Merlin ▴ 10
@merlin-15723
Last seen 20 months ago
Vancouver

Hello guys,

I am running DESeq2 to compare 4 different conditions and I have a problem with a commmand line.

dds = DESeqDataSetFromMatrix(countData = countMatrix, colData = coldata, design = ~ group + treatment +group:treatment)

although I found online many others people solved the same problem, I couldn't solve by myself. The error that I get is this

Error in checkFullRank(modelMatrix) : 
  the model matrix is not full rank, so the model cannot be fit as specified.
  One or more variables or interaction terms in the design formula are linear
  combinations of the others and must be removed.

Do you have suggestions on how to solve this?

Thank you

RNA DESeq2 • 361 views
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@mikelove
Last seen 1 day ago
United States

The vignette has suggestions on this. There’s a section devoted to this design error.

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Also I notice that many of our past interactions involve me suggesting you to read certain parts of the vignette. At this point I think it would be reasonable for you to first check the entire vignette and the function help pages before posting a support site question.

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