Hello! I have found some older posts considering whether or not to include the variable of interest while correcting with combat but they are as old as 6 years.
The current version of the sva tutorial says:
"Just as with sva, we then need to create a model matrix for the adjustment variables, including the variable of interest. Note that you do not include batch in creating this model matrix - it will be included later in the ComBat function."
But then I don't think the model actually includes the variable of interest which whould be cancer:
"modcombat = model.matrix(~1, data=pheno)".
Has this been cleared up somewhere?
Many thanks in advance!