{"action":"opened","issue":{"url":"https://api.github.com/repos/genetics-statistics/GEMMA/issues/159","repository_url":"https://api.github.com/repos/genetics-statistics/GEMMA","labels_url":"https://api.github.com/repos/genetics-statistics/GEMMA/issues/159/labels{/name}","comments_url":"https://api.github.com/repos/genetics-statistics/GEMMA/issues/159/comments","events_url":"https://api.github.com/repos/genetics-statistics/GEMMA/issues/159/events","html_url":"https://github.com/genetics-statistics/GEMMA/issues/159","id":341124989,"node_id":"MDU6SXNzdWUzNDExMjQ5ODk=","number":159,"title":"gemma 0.97 gxe analysis walt test p-value issue","user":{"login":"forevertl","id":33133724,"node_id":"MDQ6VXNlcjMzMTMzNzI0","avatar_url":"https://avatars0.githubusercontent.com/u/33133724?v=4","gravatar_id":"","url":"https://api.github.com/users/forevertl","html_url":"https://github.com/forevertl","followers_url":"https://api.github.com/users/forevertl/followers","following_url":"https://api.github.com/users/forevertl/following{/other_user}","gists_url":"https://api.github.com/users/forevertl/gists{/gist_id}","starred_url":"https://api.github.com/users/forevertl/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/forevertl/subscriptions","organizations_url":"https://api.github.com/users/forevertl/orgs","repos_url":"https://api.github.com/users/forevertl/repos","events_url":"https://api.github.com/users/forevertl/events{/privacy}","received_events_url":"https://api.github.com/users/forevertl/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-07-13T18:55:34Z","updated_at":"2018-07-13T18:55:34Z","closed_at":null,"author_association":"NONE","body":"when i ran gxe analysis using old version of gemma, i got similar p values comparing p_walt, p_lrt and p_score. Now I use the same data,same code, replicate the analysis vis gemma 0.97. I get the exact same beta and se. Very similar p_lrt as I got previously using old version of gemma. very similar p_score as I got previously using old version of gemma. but quite different p_walt vs. before. Now the p_walt columns are all around 0.1 and is quite different vs. p_socre and p_lrt. also it is different vs. previous p_walt from old vertion of gemma. my code is as below.\r\nfor chr in $(seq 22 22); do ~/gemma/bin/gemma -bfile QC_ori_order_mafp01_heals3364_chr${chr} -k relatedness_3364.sXX.txt -lmm 4 -maf 0 -c sexagebatch_3364.txt  -gxe quartile_ordinary_uascr_3364.txt  -o test_chr${chr} & done;\r\nthank you for your help and time in advance.\r\nthanks,\r\nLin"}}
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