Hi Keith,

To address both of your questions:

Interval files with the fdr value can be created by checking the option "Parse xls files into into distinct interval files".

MACS builds it model using all chromosomes, so features of one chromosome will affect the outcome from another.

For specific details of the MACS algorithm, it is probably best to contact the tool authors, the original paper, and/or the MACS documentation (see links on MACS tool form in Galaxy or search w/ google).

In particular, the FAQ hosted by the authors (http://liulab.dfci.harvard.edu/MACS/FAQ.html, near bottom) is a good place to start re: the FDR value.

We should also point out that the exact FDR calculation may differ between versions 1.3 (the version on the main Galaxy public server at http://usegalaxy.org) and MACS version 1.4 (latest released by tool authors). We noticed that the MACS changelog discusses some changes/fixes to FDR calculations. This would be a good thing to ask the MACS authors about - they might be able to give you help to understand what is in 1.3 vs 1.4.

Apologies for the late reply,

Take care,

Jen
Galaxy team

On 9/13/11 8:45 PM, Keith Giles wrote:
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
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