On Mon, Mar 1, 2010 at 6:50 AM, Johannes Rainer <[email protected]> wrote: > yes, the chipseq vignette is great, I've already adapted and used the code, > but as far as I understand the only way to identify peaks there is to use > some sort of cut-off (e.g. define islands with a lower of xx, or a x-fold > different coverage between sample to control). I'm interested in a way to > calculate a p-value for the "enrichment" of the peak, taking the nr of reads > and the depth into account.
There is a fairly simple FDR calculation that's not in the vignette yet; I'll try to put that in soon. -Deepayan > > > On Mon, Mar 1, 2010 at 3:20 PM, Michael Lawrence > <[email protected]>wrote: > >> >> >> On Mon, Mar 1, 2010 at 6:00 AM, Johannes Rainer < >> [email protected]> wrote: >> >>> and in which package is it implemented? >>> >>> >> The easiest place is in the chipseq package vignette. Just copy/paste and >> adapt that code. _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
