bias correction (an example from ChIP-seq)

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7.1 years ago

Bogdan ★ 1.4k

Dear all, I would have a more general question regarding bias correction in ChIP-seq, and i would appreciate having your suggestions.

Let's assume that someone did a ChIP-seq for a protein in 2 conditions (a. CTL, and b. KD), and we compare : 1 -- all the genes in the genome ("all") , vs 2. -- a specific subset ("subset").

After KD, there is some increase in ChIP seq intensity genome-wide (for "all" genes), although the increase on the genes in "subset" is much stronger. more specifically, looking at the MEDIAN values in each experiment, let's assume :

CTL -- "all" genes : 10

KD -- "all" genes : 20

CTL -- "subset" genes : 15

KD -- "subset" genes : 45

The question would be : what type of scaling procedure (beside computing the Z-scores), would you recommend in order to bring CTL--"all genes" and KD--"all genes" on approx the same median value ?

thank you very much,

-- bogdan

ChIP-Seq bias correction • 1.3k views

ADD COMMENT • link 7.1 years ago by Bogdan ★ 1.4k

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I recommend you to read this review: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3191340/

ADD REPLY • link 7.1 years ago by biostart ▴ 370

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