Hi all,

if I may add a more general question regarding the way to normalize the
ChIP-seq data when comparing multiple experiments. Considering the
Poisson distribution based models for peak finding, my question is the
following :

- assuming there are 2 ChIP-seq experiments :

<> minus treatment : 10 mil tags : 10000 peaks
<> plus treatment : 4 mil tags: 3000 peaks

- although the data is differently saturated, could we still compare
  10 000 peaks vs 3 000 peaks and say, for instance, 8000 peaks are lost

with the treatment, 2000 peaks remain unchanged and 1000 peaks
are gained ?
- assuming that the cut-off to call a peak is different for minus
treatment (let's say 6 tags) vs plus treatment
(let's say 4 tags), would the comparison that is described above be
statistically legitimate ? thanks a lot,

Bogdan

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