ENOCDE peaks files p-value
0
0
Entering edit mode
4.8 years ago
atsalaki ▴ 20

I downloaded peak files from ENCODE Chip-seq matrix of cell line MCF7 and TF CTCF. they have a column q-value that is the FDR, i assumed ..... Is it correct to calculate the p-value missing column values(all values are -1 because they are not provided )with this approach or it has no meaning for the identification of the binding sites of this TF? To calculate the p-value, firstly, we need to know the estimate of pi0 used to create the q-value and that's the maximum q-value or very, very close to it: pi0 = max (qvalues), then we compute m0, the estimated number of true nulls: m0 = length (qvalues) * pi0, we multiply each q-value by the proportion of true nulls expected to be under it (the inverse of how we get there from the p-value): qvalues * rank(qvalues) / m0. So the p-value for all the peak files downloaded from the ENCODE ChIP-seq Experiment matrix was calculated using the type below: p-value = q-value * rank(q-value) / (max(q-value) * length(q-value)) and then was normalized to (0-1) by applying the log() mathematical function because it was initially calculated using a –log10 scale function from the ENCODE: p-value = 1/(10^log(p-value)) I try to understand the above approach but i am having difficulties. Can someone give me a clue? thanks in advance.

ChIP-Seq p-value q-value • 1.4k views
ADD COMMENT

Login before adding your answer.

Traffic: 1761 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