According to the latest SVA vignette, the model matrix for the ComBat function should not include variables of interest, such as treatment/control but should include other covariates, such as sex. However, in previous vignettes and the SVA documentation the model matrix is defined as the "Model matrix for outcome of interest and other covariates besides batch". After trying both approaches using the vignette data, the q-values produced (again using the commands provided in the vignette) are quite different, with the model matrix consisting only of the intercept term is more conservative producing much larger values. It therefore seems that not including the variable of interest is the preferred approach. Would someone please clarify/confirm this?