Hi!

I was reading the comments and the RUV-seq Vignette, and I wondered if it is possible to use RUVg to correct more than two batches without knowing the control genes?

I understand that you might extract the empirical genes using EdgeR as described in the methodology. Still, if possible, would it make more sense to generate individual lists by the contrast between batches (1vs1)? A comparison of each batch versus the others ? or use the Housekeeping genes as controls?

Thank you very much!