To add to my post, I reread the macs documentation and it seems that the fdr is calculated based on the p value of negative peaks, regardless of their location. That is to say, a strong peak on one chromosome could be associated with a high fdr bc of an even stronger negative peak, anywhere in the genome. So, is the fdr then the percent of negative peaks relative to total peaks (pos + neg) at or below a certain p value ?
Sent from my iPhone ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
