I got the output from gemma with the -gxe flag, and I'm getting one pvalue column. Does this value correspond to the interaction term? If so, how can I get the pvalues for the genotype and environmental factors?
I ran gemma using the following commands:
gemma -bfile gemma.plink.format -k output/gemma.relatedness.matrix.cXX.txt -lmm 2 -gxe env.factor.txt -c covariate.format.txt -r2 1.0 -hwe 0 -miss 1.0 -maf 0 -notsnp -o gemma.output
FYI, the google group QA list is unavailable and the link appears to be broken.
Bests,
Lina
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To find bugs the GEMMA software developers may ask to install a
development version of the software. They may also ask you for your
data and will treat it confidentially. Please always remember that
GEMMA is written and maintained by volunteers with good
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yybgood
commented
4 weeks ago
Hi,
I got the output from gemma with the -gxe flag, and I'm getting one pvalue column. Does this value correspond to the interaction term? If so, how can I get the pvalues for the genotype and environmental factors?
I ran gemma using the following commands: gemma -bfile gemma.plink.format -k output/gemma.relatedness.matrix.cXX.txt -lmm 2 -gxe env.factor.txt -c covariate.format.txt -r2 1.0 -hwe 0 -miss 1.0 -maf 0 -notsnp -o gemma.output
FYI, the google group QA list is unavailable and the link appears to be broken.
Bests,
Lina
Describe the bug A clear and concise description of what the bug is.
To Reproduce Steps to reproduce the behavior:
Expected behavior A clear and concise description of what you expected to happen.
Screenshots If applicable, paste output to help explain your problem.
Additional context Add any other context about the problem here.
Check list:
To find bugs the GEMMA software developers may ask to install a development version of the software. They may also ask you for your data and will treat it confidentially. Please always remember that GEMMA is written and maintained by volunteers with good intentions. Our time is valuable too. By helping us as much as possible we can provide this tool for everyone to use.