I am trying to give evidence for my regulation of gene A upon gene B in cDNA Chip (i.e. hgu133a) and RNA-seq (i.e. TCGA-RNA Hiseq) dataset. I already found a high correlation between the two gene's mRNA(say coeffient R for log2 transformed expresssion is at least 0.5 in all above dataset). My assumption is if A activated, then A/B ratio will be smaller across all samples within each dataset. Now the question is I did a ratio for chip data( probeset intensity) and it worked well for survival prediction, but for RPKM data, I only found the direct Δ between A and B readcounts predict well. So do I have reason to use Δ instead of ratio for RPKM data? Does anyone have relevant reference to recommand?