sva Vignettes example qValues vs qValuesSv

[arkyl]

Hi, Thanks much for the sva package. I followed the Vignettes example using bladderEset. Without the sva adjustment, the sum(qValues<0.05) is 15193 (68% of total genes). This number is indeed as the Vignettes indicated "seems artificially high". However, after the sva adjustment, the new number sum(qValuesSv<0.05) is 14813, which is not much different from 15193. Is this the expected number, even after the sva adjustment? I just want to make sure I follow the correct steps. Thanks much. Yue