Hi everyone,

I have downloaded a set of processed data of gene expression relationship, while they offered a result of q value. Since I want to use the p value to adjust the next step, how can I convert this Q value to p value?

Thanks!

Convert Fdr Control Q-Value To P-Value

2

Entering edit mode

10.4 years ago

J.F.Jiang
▴
900

Hi everyone,

I have downloaded a set of processed data of gene expression relationship, while they offered a result of q value. Since I want to use the p value to adjust the next step, how can I convert this Q value to p value?

Thanks!

1

Entering edit mode

10.4 years ago

David Quigley
11k

I think the short answer is that you can't. One way to calculate a Q value estimate is from a distribution of P values (e.g. the way Storey's qvalue works), but I don't think there is any way to reconstruct the P value distribution from a set of estimated Q values. You should calculating the P values directly if that's what you want. The manual to the qvalue package has more information about what a Q value is and how it can be calculated, which you might want to read.

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Is it possible that your dataset was analyzed by a method that does not produce p-values? For example, baySeq, a tool for testing differential expression in RNA-Seq data, produces posterior probabilities from a Bayesian analysis and calculates FDR directly from them. The nature of the calculations is such that no p-value is involved.

How did you get your Q values ?