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I have a analysis in edgeR, but it ended by error. This is my data:
Sample treat factor1 factor2
s1 CT 1 c1
s2 CT 1 c2
s3 CT 2 c3
s4 CT 2 c4
s5 CT 1 c2
s6 CT 2 c3
s7 CT 2 c4
s8 CT 1 c5
s9 CT 1 c6
s10 CT 2 c7
s11 treatmetn 2 c3
s12 treatmetn 2 c4
s13 treatmetn 1 c5
s14 treatmetn 2 c6
s15 treatmetn 1 c7
s16 treatmetn 2 c8
s17 treatmetn 1 c9
s18 treatmetn 2 c4
s19 treatmetn 2 c5
s20 treatmetn 2 c6
s21 treatmetn 1 c7
s22 treatmetn 2 c8
I used this formula for analysis
--formula "treat+factor1+factor2" \
at the end I have this error:
Error in glmFit.default(sely, design, offset = seloffset, dispersion = 0.05, : Design matrix not of full rank. The following coefficients not estimable: factor2C8 Calls: estimateDisp ... estimateDisp -> estimateDisp.default -> glmFit -> glmFit.default Execution halted