Hi! I've used the DESeq package and now I'm trying the DEXSeq one. In the DESeq package I can access the baseMean, baseMeanA, baseMeanB values before doing the analysis, but using the DEXSeq package, I only get the meanBase value. How can I get the baseMeanA baseMeanB values using the DEXSeq package? Thanks! []s Mariana -- output of sessionInfo(): > head(res1) geneID exonID dispersion pvalue padjust meanBase rajko.90nt.slRNA-3.1.1:E001 rajko.90nt.slRNA-3.1.1 E001 1.760727e-02 NA NA 152.07637815 rajko.90nt.slRNA-31.1.1:E001 rajko.90nt.slRNA-31.1.1 E001 6.178367e-02 NA NA 19.12018340 rajko.90nt.slRNA-39.1.1:E001 rajko.90nt.slRNA-39.1.1 E001 5.967594e-02 NA NA 19.95246225 rajko.90nt.slRNA-41.1.1:E001 rajko.90nt.slRNA-41.1.1 E001 1.668097e+01 NA NA 0.05795718 rajko.90nt.slRNA-45.1.1:E001 rajko.90nt.slRNA-45.1.1 E001 1.000000e+08 NA NA 0.00000000 rajko.90nt.slRNA-46.1.1:E001 rajko.90nt.slRNA-46.1.1 E001 6.830553e-01 NA NA 1.43811945 log2fold(all/sl) rajko.90nt.slRNA-3.1.1:E001 NA rajko.90nt.slRNA-31.1.1:E001 NA rajko.90nt.slRNA-39.1.1:E001 NA rajko.90nt.slRNA-41.1.1:E001 NA rajko.90nt.slRNA-45.1.1:E001 NA rajko.90nt.slRNA-46.1.1:E001 NA -- Sent via the guest posting facility at bioconductor.org.