Hi Gordon, Thanks for your quick answer. I used trend=TRUE 'cause you posted in Bioconductor that it's a good strategy if you are not filtering for genes with low counts, as this strategy is devoted to model a good mean-variance trend for genes on the low expression range. This is the message I got, but correct me if I am wrong, please. Post: https://stat.ethz.ch/pipermail/bioconductor/2013-May/052816.html If, as you say, voom already handles this issue, excellent, there is no need to set trend=TRUE in eBayes function. However, if I have already performed the analysis with trend=TRUE in eBayes function, do you think that this bears heavily on the DE analysis results? If so, the bias may go in which direction: increasing the number of false positives or false negatives? I'm asking that for practical reasons, so as to decide to repeat the analysis again or use the results I have already produced. Thanks a lot Meri Meritxell Oliva PhD student IBB (Biotechnology and Biomedicine Institute) Comparative and Functional Genomics group Campus Universitari - 08193 Bellaterra Cerdanyola del Vall?s - Barcelona