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)

and

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

I have never seen that error message from eBayes() for any real dataset. As far as I know, the error message could only arise from a dataset for which an entire row of expression values were all NA. In other words, a pretty weird dataset.

You obviously can't expect to do any analysis for a gene or protein when all the expression values are NA, so such rows should be removed.

Neither of the code chunks that Google made you check are at all relevant to the error message. The error message has nothing to do with the design matrix. Besides, if the design matrix was not of full rank, you would already know because limma checks for that automatically.