Cufflinks bias correction
Hi all
My boss asked me to do correction for my data generated from cuffdiff to eliminate bias.
When I was doing cuffdiff, I wrote -b <genome.> in my cuffdiff command line. As I know it also does bias correction.
Then I told my boss, cufflinks does correction. He asked me, what kind of test does it use for correction? I did not know the answer. He told me: there are many tests like t-test and ANOVA for correction.
Does anyone know what kind of test is used in cufflinks for bias correction?
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I think it would be a good idea if you first ask your boss what he means with "bias".
AFAIK, Cufflinks uses the genome-sequence to correct for sequence-bias in your data. It looks (please correct me) for over-represented sequences and adjusts the FPKM value accordingly.