Question: PLINK/SEQ SKAT gives different p-values depending on number of tests run
gravatar for p0078005
3.3 years ago by
p00780050 wrote:

We are using PSEQ to analyse rare variants at a gene-based level. I like the interface and the output from PSEQ but have noticed that if I run SKAT alone, I get a different p-value from if I run SKAT and (for example) C-alpha in the same line.

The input files are exactly the same, it is just the number of tests run that differ. Can anyone tell me if PSEQ uses a project-wide p-value adjustment by default (this is the only explanation I can think of to explain this).

Thanks DIanne

pseq plinkseq skat • 1.2k views
ADD COMMENTlink modified 2.6 years ago by Biostar ♦♦ 20 • written 3.3 years ago by p00780050

As far as I know SKAT will return a different p-value every time you run it, regardless of running other tests. But that's the case if you just run SKAT in R. Not sure about PSEQ.

ADD REPLYlink written 3.3 years ago by WouterDeCoster45k
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