I was wondering if I could get some help with a copy number variation analysis I am running. I am currently using ChAMP to run the analysis and I am fairly new at it. Is there a way to run a normalization and batch effect correction on the intensity values to clean up the data before I run champ.CNA on these values? I have been using champ.runCombat() and champ.norm() but both work with the beta values not intensity values.
Any help would be much appreciated and thanks in advance!