Hi, I'm currently looking over RNASeqV2 Level 3 data from TCGA. I was wondering if there were any pitfalls to doing a quick and dirty comparison of the RPKM values for say matched Normal samples vs the RPKM values for matched tumor samples for x genes. Can I just compare them outright from normal set to tumor set? Does it really matter that there are more tumor samples if I simply compare them as groups?
PS I know depending on the tissue there are certain subtypes listed under the same cancer so I sometimes seperate out by that ie ductal and lobular for breast invasive carcinoma.