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?