Question

DiffBind cut off clarification

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onkarnath89 • 0

@onkarnath89-11711

Last seen 8.1 years ago

I am using diffbind to find differential peaks between different samples obtained in different conditions. The manual says that dba.analyze implies a FDR cut off of 0.05 and DEseq2 implies a cut off of 0.1.

So In my understanding as dba.analyze uses DESeq2 thus the differential peaks are found at a cut off of 0.1 and then dba.analyze screens it further at cut off 0.05.

But the results I obtained seems to be screened at 0.1 FDR. Kindly clarify

I also want to know if there a way to screen on some user defined P-value or FDR value.

diffbind differential gene expression • 2.7k views

ADD COMMENT • link updated 8.1 years ago by Gord Brown ▴ 670 • written 8.1 years ago by onkarnath89 • 0

score 0 · Answer 1 · 2016-10-20

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Gord Brown ▴ 670

@gord-brown-5664

Last seen 3.9 years ago

United Kingdom

Hi,

P-value and FDR calculations are done for all peaks, whether you use DESeq, DESeq2, or EdgeR: the threshold only affects reporting. You can choose a threshold when you call dba.report with the "th" parameter: including "th=0.05" for example will set the FDR to 0.05. You can place a threshold on the p-value instead of the FDR by setting "bUsePval=TRUE" when calling dba.report.

Hope this helps...

- Gord

ADD COMMENT • link 8.1 years ago Gord Brown ▴ 670

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And the default reporting FDR is 0.1, just for the record.

ADD REPLY • link 8.1 years ago Gord Brown ▴ 670

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As of DiffBind 2.0, the default FDR cutoff for reporting and plotting is 0.05 for all methods. As Gord says, you can specify your desired cutoff explicitly in all the calls. For example, calling dba.report() with th=1 will return a report that includes statistics for every peak. Also, you can change the default FDR cutoff for a project by setting DBA$config$th to the desired value.

ADD REPLY • link 8.1 years ago Rory Stark ★ 5.2k