Use normalized counts to generate Fold change?

Question

[tud55122]

Hi,

Just want to make sure. I have two batches of RNA-seq and am trying to normalize based on housekeeping genes to minimum batch effect. Should I use normalized counts after RUVSeq correction to generate RPKMs and Fold Change? According to the introduction from RUVSeq, original counts are recommended to be used for generating differentially expressed genes.

Thanks, Hang