Question: Standard Fdr Threshold In Chip-Seq & How To Co-Relate It To Q-Value [Macs14]
0
gravatar for Sukhdeep Singh
7.8 years ago by
Netherlands
Sukhdeep Singh10k wrote:

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 • 5.1k views
ADD COMMENTlink written 7.8 years ago by Sukhdeep Singh10k

q-value is FDR corrected p-value.

ADD REPLYlink written 7.8 years ago by Arun2.3k

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 REPLYlink modified 7.8 years ago • written 7.8 years ago by Sukhdeep Singh10k
1
gravatar for Sean Davis
7.8 years ago by
Sean Davis26k
National Institutes of Health, Bethesda, MD
Sean Davis26k wrote:

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 COMMENTlink written 7.8 years ago by Sean Davis26k

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 REPLYlink written 7.8 years ago by Sukhdeep Singh10k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1223 users visited in the last hour