Hi, I'm analyzing an RNAseq experiment with DeSeq2, but I have a problem. I have two groups (treated and untreated) composed by the same subjects. I would like to see if the treatment caused any RNA expression alteration, making a paired analysis.
My data file is structured with 5 columns:
Sample Treatment Subject Age Sex
1 Y A 31 M
2 N A 30 M
3 Y B 27 F
4 N B 25 F
5 Y C 47 M
5 N C 46 M ...
I would like to include all the variables in the DeSeq analysis; however, when I make ~ Age + Sex + Subject + Treatment, I got the message:
However I then get the error:
Error in DESeqDataSet(se, design = design, ignoreRank) : 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
How can I solve the issue?