{"action":"created","issue":{"url":"https://api.github.com/repos/FCP-INDI/C-PAC/issues/404","labels_url":"https://api.github.com/repos/FCP-INDI/C-PAC/issues/404/labels{/name}","comments_url":"https://api.github.com/repos/FCP-INDI/C-PAC/issues/404/comments","events_url":"https://api.github.com/repos/FCP-INDI/C-PAC/issues/404/events","html_url":"https://github.com/FCP-INDI/C-PAC/issues/404","id":50091294,"number":404,"title":"Group Analysis [Measure_Mean]: v 0.3.7.","user":{"login":"msk1105","id":8195791,"avatar_url":"https://avatars.githubusercontent.com/u/8195791?v=3","gravatar_id":"","url":"https://api.github.com/users/msk1105","html_url":"https://github.com/msk1105","followers_url":"https://api.github.com/users/msk1105/followers","following_url":"https://api.github.com/users/msk1105/following{/other_user}","gists_url":"https://api.github.com/users/msk1105/gists{/gist_id}","starred_url":"https://api.github.com/users/msk1105/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/msk1105/subscriptions","organizations_url":"https://api.github.com/users/msk1105/orgs","repos_url":"https://api.github.com/users/msk1105/repos","events_url":"https://api.github.com/users/msk1105/events{/privacy}","received_events_url":"https://api.github.com/users/msk1105/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"sgiavasis","id":4644673,"avatar_url":"https://avatars.githubusercontent.com/u/4644673?v=3","gravatar_id":"","url":"https://api.github.com/users/sgiavasis","html_url":"https://github.com/sgiavasis","followers_url":"https://api.github.com/users/sgiavasis/followers","following_url":"https://api.github.com/users/sgiavasis/following{/other_user}","gists_url":"https://api.github.com/users/sgiavasis/gists{/gist_id}","starred_url":"https://api.github.com/users/sgiavasis/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sgiavasis/subscriptions","organizations_url":"https://api.github.com/users/sgiavasis/orgs","repos_url":"https://api.github.com/users/sgiavasis/repos","events_url":"https://api.github.com/users/sgiavasis/events{/privacy}","received_events_url":"https://api.github.com/users/sgiavasis/received_events","type":"User","site_admin":false},"milestone":{"url":"https://api.github.com/repos/FCP-INDI/C-PAC/milestones/2","labels_url":"https://api.github.com/repos/FCP-INDI/C-PAC/milestones/2/labels","id":862597,"number":2,"title":"v0.3.9 Release","description":"","creator":{"login":"sgiavasis","id":4644673,"avatar_url":"https://avatars.githubusercontent.com/u/4644673?v=3","gravatar_id":"","url":"https://api.github.com/users/sgiavasis","html_url":"https://github.com/sgiavasis","followers_url":"https://api.github.com/users/sgiavasis/followers","following_url":"https://api.github.com/users/sgiavasis/following{/other_user}","gists_url":"https://api.github.com/users/sgiavasis/gists{/gist_id}","starred_url":"https://api.github.com/users/sgiavasis/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sgiavasis/subscriptions","organizations_url":"https://api.github.com/users/sgiavasis/orgs","repos_url":"https://api.github.com/users/sgiavasis/repos","events_url":"https://api.github.com/users/sgiavasis/events{/privacy}","received_events_url":"https://api.github.com/users/sgiavasis/received_events","type":"User","site_admin":false},"open_issues":19,"closed_issues":4,"state":"open","created_at":"2014-11-11T23:32:37Z","updated_at":"2015-01-26T23:07:53Z","due_on":"2014-12-19T05:00:00Z","closed_at":null},"comments":2,"created_at":"2014-11-25T22:12:56Z","updated_at":"2015-01-26T23:10:09Z","closed_at":null,"body":"Even when I select only \"smoothed & zscore std\" (not \"raw score\") for group analysis, CPAC seems to include \"Measure_Mean\" as an EV. That is, after uploading an EV file, \"Measure_Mean\" is automatically added to the Model Setup box (and also to Design Matrix Formula). See the image below. \r\n\r\nAs \"Measure_Mean\" should be included as an EV *only* when we use raw score (to covary out \"Measure_Mean\" at the group level), I want to double check if CPAC can add \"Measure_Mean\" only when raw score is selected/used by users. \r\n\r\nMaki \r\n\r\n![slide1](https://cloud.githubusercontent.com/assets/8195791/5192517/1692c3a4-74c6-11e4-8ae0-9f3477cea315.png)\r\n\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/FCP-INDI/C-PAC/issues/comments/71558416","html_url":"https://github.com/FCP-INDI/C-PAC/issues/404#issuecomment-71558416","issue_url":"https://api.github.com/repos/FCP-INDI/C-PAC/issues/404","id":71558416,"user":{"login":"ccraddock","id":1725272,"avatar_url":"https://avatars.githubusercontent.com/u/1725272?v=3","gravatar_id":"","url":"https://api.github.com/users/ccraddock","html_url":"https://github.com/ccraddock","followers_url":"https://api.github.com/users/ccraddock/followers","following_url":"https://api.github.com/users/ccraddock/following{/other_user}","gists_url":"https://api.github.com/users/ccraddock/gists{/gist_id}","starred_url":"https://api.github.com/users/ccraddock/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ccraddock/subscriptions","organizations_url":"https://api.github.com/users/ccraddock/orgs","repos_url":"https://api.github.com/users/ccraddock/repos","events_url":"https://api.github.com/users/ccraddock/events{/privacy}","received_events_url":"https://api.github.com/users/ccraddock/received_events","type":"User","site_admin":false},"created_at":"2015-01-26T23:10:09Z","updated_at":"2015-01-26T23:10:09Z","body":"I think that this is a documentation issue. When z-score is included, please do not include automatically include measure_mean in the model specification equation, but do continue to calculate the measure mean and add it to the internal phenotype file. This way a user can include measure_mean with z-score if they like. This requires that the model can only run on z-scored derivatives or non-z-scored derivatives and not both. Please verify that this is the case."}}