While running plink, I got below error:
FEXACT error 3
plink-1.07-x86_64/plink --noweb --file inputplinefile --pheno input.phe --fisher
Does anybody have any idea of it?
It is a problem probably related to the size of the matrix you are testing.
One option would be to see if you can perform separate tests on subsets of your data. This would also rule out the hypothesis of malformed input.
One option could be using a newer version of plink, since apparently they abandoned the FEXACT algorithm to compute Fisher test and this may solve your problem. See here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4342193/
Will try to use new version
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