Hi James, thanks for the explanation. I do not really understand the columns yet. Shouldn't the FC be printed for every comparison as is done for the Coef-columns? I just get one A-column. Is there any way of printing the results to a file with the same columns as in topTable()? I checked in the output after the "eBayes"-function and saw that there was a variable called "Amean". Does it mean that the A-column in my output file after "write.fit" is the mean of all the FCs in the comparisons between the group of treats I am analysing? What I really want to have in the output is a p-value column, an FC column and an adjusted p-value column for each comparison. Best regards [[alternative HTML version deleted]]