Question: Cufflinks bias correction
gravatar for Xin
5.3 years ago by
Xin60 wrote:

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?

rna-seq • 2.0k views
ADD COMMENTlink modified 4.0 years ago by Biostar ♦♦ 20 • written 5.3 years ago by Xin60

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

ADD REPLYlink written 5.3 years ago by Martombo2.7k

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.

ADD REPLYlink written 5.3 years ago by michael.ante3.6k
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