Second normalization for TCGA data
Hi, I'm now using the TCGA RNASeq data (Illumina Genome Analyzer) to do some screening for new interesting candidate genes related to cancer. However, I plotted three housekeeping genes' expression in the dataset and found out that one of them does not have the same expression level in tumor and normal samples. So I was wondering if I can do the screening again, but this time with TCGA data normalized to the housekeeping gene's expression, knowing that TCGA's RNASeq data are already normalized?
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How did you determine that your gene of interest is a housekeeping gene? These genes are not always as constant, depending on the condition/tissue/treatment.
Please excuse me, I didn't explain it clearly. My gene of interest is not a housekeeping gene, but I do RT-PCR and ddCT with a housekeeping gene after to validate the induction of the expression of my gene of interest in tumor tissues compared to normal tissues. So at first I just used TCGA's normalized dataset to do my screening. Then now I tried to do screening with TCGA's data, normalized to the expression of a housekeeping gene (which doesn't have the same expression average between tumor and normal tissues), and I obtained different candidate genes but I don't know if I can do this second normalization or not.