EQTL FDR vs raw p-value
0
0
Entering edit mode
4 weeks ago

Hello,

I am using with GWAS data and use the FUMA-online annotation tool for this task. Amongst other things, I am especially interested in mapping eqtls from GTEx to my variants. Here comes my question: FUMA reports for each eqtl the FDR and the p-value.

How would you in general evaluate an eqtl-association: By FDR or by the raw p-value? For some variants the FDR is lower than the p-value and for others the other way around (does this mean sth.?)

I think that FDR makes more sense --> My strategy would be to filter for eqtls with a FDR < 0.05 Does this make sense to you?

Best,

Andreas

FUMA EQTL • 239 views
ADD COMMENT
1
Entering edit mode

As for me - absolutely. In general, you should always prefer FDR over raw p-values (given that you do this type of analysis - frequentist multiple testing).

ADD REPLY
0
Entering edit mode

For some variants the FDR is lower than the p-value and for others the other way around (does this mean sth.?)

Isn't that impossible ? As far as I know, the FDR-corrected pvalue is, by definition, always higher (or equal in very specific cases) than the uncorrected pvalues.

ADD REPLY
0
Entering edit mode

I rechecked it and it is the q-value and actually not the FDR, which is reported by this tool. Sorry for this! So in some cases the q-value is lower than the p-value. However, still I don't know if this makes sense and if yes, if it makes sense to filter for q < 0.05?

ADD REPLY
0
Entering edit mode

It would be very strange for me to call some value q-value in the context of statistics and denote something other than FDR estimation.

ADD REPLY

Login before adding your answer.

Traffic: 1007 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