Re: [Useq-users] variation between peak callers

[David N. <dav...@gm...>]

Hello Noboru,

The simple answer is because they use different methods with different
filters.  Calling strong peaks is easy, accurately calling weak peaks is
difficult.  Furthermore, FDR estimations are often quite variable so
comparing list at a single FDR of say 1% will be misleading.  The error is
often +/- 2-10 fold!

-cheers, D 


On 3/23/11 6:04 PM, "Noboru Jo Sakabe" <ns...@uc...> wrote:

>     Hi David, would you comment on why running different peak callers on
> the same data results in different peaks?
>     I noticed that for PolII, I didn't have this problem. But for TFs
> that, I assume, have weaker enrichment, this seems to be common. I just
> ran Useq on published data and I obtained low overlap, ~20%, at 1bp.
> But, both sets make biological sense (although GO for Useq peaks/genes
> gave me fewer terms for the tissue), peaks are generally conserved,
> overrepresentation of peaks on the TSS, expression levels on the tissue
> make sense, peaks cluster as a sharp peak around the TSS.
>     I always assumed that when the IP is not highly enriched, such
> variation occurs. Maybe you can say something else based on your experience?
>     I mean, is this something we have to live with, or is it something
> wrong I'm doing and I should see higher overlap?
>     Thanks a lot!
> 
> noboru
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