Hello My microarrays were processed in batches. I would like to remove batch effect using ComBat. But I also want to adjust for unknown sources of noise using sva. Is there a way of combining these two methods? I could run ComBat first, get the ComBat-adjusted matrix, and run sva on this, but I am concerned if it is bad practice to run a second adjustment on data which has already been adjusted by a different package. Is it possible perhaps to include the surrogate variables from SVA in the model matrix for ComBat? Or is there a better way of combining the methods? Please note that I would prefer to use ComBat to remove batches, rather than use batch as an adjustment variable in sva, as ComBat does a better job of removing batch effect from my data. Thank you! Nasir [[alternative HTML version deleted]]