Get p-value for each feature-variant test
liangyy opened this issue · 7 comments
Hi Natsuhiko,
I have a question about obtaining the raw p-value of the test. I am not sure if the q-value reported is always done by permutation. I am wondering if it is possible to get the raw p-value of each test (and presumably shut down permutation since it is not necessary for this setting).
Thank you very much!
Yanyu
Hi Yanyu,
The Q-value is based on the Benjamini-Hochberg method, but not permutation. This is adjusting multiple testing for each feature.
Best regards,
Natsuhiko
Hi Natsuhiko,
Thanks for your explanation! I am wondering if rasqual
can output raw p-value w/o transforming it to q-value. If not, can I do something like p.val = q.val * rank(q.val, ties.method = 'max') / length(q.val)
to get a rough estimate on p-value (I guess it is upper bound of p-value)?
Thanks!
Yanyu
Hi Yanyu,
You can calculate the p-value from the chi-square statistic on the 11th column of the output, e.g., pchisq(col11, 1, lower=F) on R.
Best regards,
Natsuhiko
Hi Natsuhiko,
Thanks for the clarification! I will close the issue.
Yanyu
A followup on this, when pchisq(col11,1,lower=F) is used to get p-values, do these p-values need to be multiplied by 2 before multiple testing correction?
You don't need to do so, the log likelihood ratio is already multiplied by 2 and this is one tailed test.
Best regards,
Natsuhiko
Thanks for your helpful (and quick) reply