MACS: overalll expected FDR?

Question

[linuxjoga]

For a university course I have to analyse some data using MACS14. I have been able to answer most of the questions. However, the exercises ask for the "overall expected False Discovery Rate" of my data?

Could anybody explain me what is meant by this and where I can find it in the MACS-output files? I have been spending the last 6 hours trying to figure this out, but still have no idea. (Every documentation just talks about the local FDR for each peak).

Unfortunately, the teacher is not available for questions and the deadline is approaching, so I would be very grateful for some hint!

Answer 1

[Ming Tommy Tang]

you should find a column called FDR in in the .xls file outputted by MACS14.

[linuxjoga]

Yes, but in this way, I get the FDR for every single peak - I rather need one single number for the entire set of data.

[Ming Tommy Tang]

check whether the ChIP peaks also show up in the negative peaks.

[linuxjoga]

They don't.