Plink: Fisher's Exact test ERROR: FEXACT error 3

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4.6 years ago

Sudhir Jadhao ▴ 70

Hello Everyone,

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?

Plink Association study • 1.7k views

ADD COMMENT • link updated 4.6 years ago by ATpoint 82k • written 4.6 years ago by Sudhir Jadhao ▴ 70

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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/

ADD REPLY • link 4.6 years ago by Fabio Marroni ★ 3.0k

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Thank Fabio!! Will try to use new version

ADD REPLY • link 4.6 years ago by Sudhir Jadhao ▴ 70

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