I am using RUVseq for removing unwanted variation with a number of housekeeping genes as control genes but I got this error:
Error in Ycenter[, cIdx] : invalid subscript type 'list'
This is the code I use:
batchCorrectedSet <- RUVg(as.matrix(countTable), control.genes, k=1)
Also, if I remove "as.matrix" from the command I got this error:
unable to find an inherited method for function ‘RUVg’ for signature ‘"data.frame", "data.frame", "numeric"’
Any help will be appreciated. Thank you.