[BioC] DEseq for chip-seq data normalisation

Davide Cittaro cittaro.davide at hsr.it
Wed Nov 6 10:18:40 CET 2013

Dear Lucia,

On 05/nov/2013, at 13:57, Giuseppe Gallone <giuseppe.gallone at dpag.ox.ac.uk> wrote:

>> I do not recommend doing the peak calling with the pooled data.After
>> doing several ChIP-seq experiments with replicates I have observed that
>> a lot of peaks, even ones with high z-scores/low p-values, do not show
>> up in more than one replicate (but maybe this is particular to my type
>> of experiments).  Merging all the peaks leads to a high number of false
>> positives. So you need to integrate the peak locations into a single
>> file but make sure you have a minimum number of carriers for each peak,
>> I usually do presence in at least 2 of the replicates.

This sounds reasonable and, indeed, I have a similar anedoctical experience. Do you have some data/benchmarks supporting this claim?


Davide Cittaro, PhD

Coordinator of Bioinformatics Core
Center for Translational Genomics and Bioinformatics
Ospedale San Raffaele
Via Olgettina 58
20132 Milano

Office: +39 02 26439211
Mail: cittaro.davide at hsr.it
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