Standard Fdr Threshold In Chip-Seq & How To Co-Relate It To Q-Value [Macs14]
1
0
Entering edit mode
11.9 years ago

Hi,

My first question is, what is the standard measure of FDR (if any) while calling peaks in ChIP-Seq.

And, how to co-relate the emperical FDR from Macs14 (peak caller) to a q-value threshold. Is it just, empFDR=(q-value/10)*100 or one cannot make such remarks.

Can we modulate this threshold on the case to case basis. There might be a case, when your protein is low expressed, so the enrichment is low. And when you call peaks, they pass the p-value threshold, but the enrichment at most postions is same or less than the control, so FDR is high. What to do in that case.

Cheers

P.S. The empirical FDR in Macs 14 is defined as Number of control peaks / Number of ChIP peaks.

macs chip-seq • 7.3k views
ADD COMMENT
0
Entering edit mode

q-value is FDR corrected p-value.

ADD REPLY
0
Entering edit mode

yeah I agree and this led me to read this post about p,FDR and q values and these lines say the thing

a p-value of 0.05 implies that 5% of all tests will result in false positives. An FDR adjusted p-value (or q-value) of 0.05 implies that 5% of significant tests will result in false positives. The latter is clearly a far smaller quantity.

ADD REPLY
1
Entering edit mode
11.9 years ago

The false discovery rate is just that. There is no obvious cutoff for such a value, but the biological interpretation is meant to be relatively clear. If a "cutoff" of 0.05 is used, 95% of the results are not false discoveries. Following that reasoning, any cutoff <1 is justifiable, but it may be impractical.

ADD COMMENT
0
Entering edit mode

Thanks Sean, so one can say that a protein is low expressed and using a threshold of 0.5 (50% chance the peaks might be wrong) will be fine

ADD REPLY

Login before adding your answer.

Traffic: 2699 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6