Im performing diff expression analysis for proteome data with LIMMA. As heteroscedasticity is present in my data and could not be corrected with VOOM (question here) I would like to try eBayes with the option trend = T. Unfortunately I get the error: Error in fitFDist(var, df1 = df, covariate = covariate) : NA covariate values not allowed.
A google search made me check for:
Matrix::rankMatrix(design_dateProc) == ncol(design_dateProc)
any(colSums(design_dateProc) == 0)
However, first one is TRUE, second one is FALSE, ergo no problem there. I also checked if my blocking of batch effects is a problem but its the same if I don't block for it.
Any ideas what to do here? Thanks a lot! Sebastian