{"action":"opened","issue":{"url":"https://api.github.com/repos/DReichLab/EIG/issues/24","repository_url":"https://api.github.com/repos/DReichLab/EIG","labels_url":"https://api.github.com/repos/DReichLab/EIG/issues/24/labels{/name}","comments_url":"https://api.github.com/repos/DReichLab/EIG/issues/24/comments","events_url":"https://api.github.com/repos/DReichLab/EIG/issues/24/events","html_url":"https://github.com/DReichLab/EIG/issues/24","id":301265222,"number":24,"title":"Decimal places in EigenStrat p-values?","user":{"login":"cizydorczyk","id":22860940,"avatar_url":"https://avatars1.githubusercontent.com/u/22860940?v=4","gravatar_id":"","url":"https://api.github.com/users/cizydorczyk","html_url":"https://github.com/cizydorczyk","followers_url":"https://api.github.com/users/cizydorczyk/followers","following_url":"https://api.github.com/users/cizydorczyk/following{/other_user}","gists_url":"https://api.github.com/users/cizydorczyk/gists{/gist_id}","starred_url":"https://api.github.com/users/cizydorczyk/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cizydorczyk/subscriptions","organizations_url":"https://api.github.com/users/cizydorczyk/orgs","repos_url":"https://api.github.com/users/cizydorczyk/repos","events_url":"https://api.github.com/users/cizydorczyk/events{/privacy}","received_events_url":"https://api.github.com/users/cizydorczyk/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":0,"created_at":"2018-03-01T03:25:42Z","updated_at":"2018-03-01T03:25:42Z","closed_at":null,"author_association":"NONE","body":"Hello,\r\n\r\nI have successfully managed to run EigenStrat (smartpca and smarteigenstrat) on a collection of ~34k SNPs (I am aware of the potential loss of power). I ran smartpca on all of the 34k SNPs (which have been filtered from a larger SNP dataset to remove linkage disequilibrium, and a MAF 0.05 filter applied), and then tested all 34k SNPs for association.\r\n\r\nWhen looking at the output, however, I note that p-values only down to 4 decimal places are reported, with many loci having reported values of '0.000' in my .chisq output file.\r\n\r\nIs there any reason why the p-values seem to go no lower than 4 decimal places? I find it hard to believe that are that many significant loci in my dataset, especially since other methods I have tried find very few if any, and the threshold for a simple Bonerroni correction I wish to use at this point is 10^-5.\r\n\r\nI have read over the documentation several times, but cannot find any mention of this issue/any options concerning this output, or why it might be occurring.\r\n\r\nI feel as though I must be overlooking something, or perhaps not running EigenStrat correctly, although I had no trouble running smartpca.perl or smarteigenstrat.perl. Note that I used ped/map files as input.\r\n\r\nAny help in understanding this issue is much appreciated!\r\n\r\nThank you,\r\nConrad Izydorczyk"}}
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