Hi!

I’m using the RUV2( ) function in the “ruv” package to process my micro-array data. Could anyone please tell me how I can get the normalised data? I can’t see it under “Value” in the help page of RUV2( ). (RUVg( ) in the "RUVSeq" package returns the normalised data.) I understand that I shouldn’t use the normalised data for any downstream analysis; I need the normalised data only for the purpose of creating PCA plots so that I know whether the samples cluster properly after RUV-2 algorithm.

Cheers

Paul

You should be able to access normalised counts from normCounts() e.g normCounts(set)