Hiii dear friends..
I used TopHat and CUfflinks suite applications to find out differential expression.
I just followed the QC -> TopHat -> Cufflinks -> Cuffmerge -> Cuffdiff -> Cummerbund
Then my boss asked me: " Did you do normalization?! "; "Did you use any t-test or Baysian or other tests to normalize the data?" I said No.
What should I normalize and why??
If any Cufflinks tools does normalization, what kind of test it uses?