Cufflinks bias correction

Question

[Xin]

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?

[Martombo]

I think it would be a good idea if you first ask your boss what he means with "bias".

[michael.ante]

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.