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genetics-statistics / GEMMA

Genome-wide Efficient Mixed Model Association
https://github.com/genetics-statistics/GEMMA
GNU General Public License v3.0
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gxe issue #146

Closed jsmithcvm closed 6 years ago

jsmithcvm commented 6 years ago

We have been having an issue with the gxe command within univariate mixed model associations. The command line we are using consists of -g genotypefile -p phenotypefile -n 1 -k kinshipmatrix -a annotationfile -lmm 4 -gxe environmentalcovariate -c fixedcovariate -o outputfilename

For the gxe environmental variable it is formatted as a single column consisting of Zone1 through Zone9 The fixed covariate file is sex based with the intercept column first, sex (M or F) in the second column

Prior to this we had done a linear mixed model without the gxe variable, but with a covariate file that had intercept, zone, sex columns in that order. The linear mixed model without the gxe option runs fine with what appears to be a logical output.

The gxe results have nan outputs for every p-value, se, and beta as well. The l_remle and l_mle outputs are all 1.0e+05 indicating all genotype interaction and no environmental interaction. There are no error messages being displayed. We are using version 0.96.

pcarbo commented 6 years ago

@jsmithcvm I will respond to your email posted to the Google Group.