Plink: Fisher's Exact test ERROR: FEXACT error 3
0
0
Entering edit mode
19 months ago

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 • 676 views
ADD COMMENT
0
Entering edit mode

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
0
Entering edit mode

Thank Fabio!! Will try to use new version

ADD REPLY

Login before adding your answer.

Traffic: 1756 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