Question: Second normalization for TCGA data
gravatar for yuyu
4.3 years ago by
yuyu0 wrote:

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?

ADD COMMENTlink modified 4.2 years ago by Biostar ♦♦ 20 • written 4.3 years ago by yuyu0

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.

ADD REPLYlink written 4.3 years ago by WouterDeCoster44k

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.

ADD REPLYlink written 4.3 years ago by yuyu0
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