DESeq and checkFullRank(modelMatrix)

NDUFB11 · 04-18-2019, 06:22 AM

Hello guys,

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

Code:

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

Code:

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

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04-18-2019, 06:22 AM	#1
NDUFB11 Member Location: Italy Join Date: Jul 2017 Posts: 34	DESeq and checkFullRank(modelMatrix) Hello guys, I am running DESeq2 to compare 4 different conditions and I have a problem with a commmand line. Code: 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 Code: 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