{"action":"created","issue":{"url":"https://api.github.com/repos/PF2-pasteur-fr/SARTools/issues/20","repository_url":"https://api.github.com/repos/PF2-pasteur-fr/SARTools","labels_url":"https://api.github.com/repos/PF2-pasteur-fr/SARTools/issues/20/labels{/name}","comments_url":"https://api.github.com/repos/PF2-pasteur-fr/SARTools/issues/20/comments","events_url":"https://api.github.com/repos/PF2-pasteur-fr/SARTools/issues/20/events","html_url":"https://github.com/PF2-pasteur-fr/SARTools/issues/20","id":169588858,"number":20,"title":"error in statistics tables","user":{"login":"AlexandraBomane","id":9327758,"avatar_url":"https://avatars.githubusercontent.com/u/9327758?v=3","gravatar_id":"","url":"https://api.github.com/users/AlexandraBomane","html_url":"https://github.com/AlexandraBomane","followers_url":"https://api.github.com/users/AlexandraBomane/followers","following_url":"https://api.github.com/users/AlexandraBomane/following{/other_user}","gists_url":"https://api.github.com/users/AlexandraBomane/gists{/gist_id}","starred_url":"https://api.github.com/users/AlexandraBomane/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/AlexandraBomane/subscriptions","organizations_url":"https://api.github.com/users/AlexandraBomane/orgs","repos_url":"https://api.github.com/users/AlexandraBomane/repos","events_url":"https://api.github.com/users/AlexandraBomane/events{/privacy}","received_events_url":"https://api.github.com/users/AlexandraBomane/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2016-08-05T11:38:44Z","updated_at":"2016-08-05T13:16:33Z","closed_at":null,"body":"Hello !\r\n\r\nI have a problem with my statistics tables obtained after running SARTools with DESeq2 package.\r\nThe calculations made in FoldChange and log2FoldChange fields seem incorrect.\r\n\r\nHere an entry for example : \r\n\r\nId : YAL002W\r\ns1-condA : 17\t\r\ns2-condA : 23\t\r\ns3-condB : 35\t\r\ns4-condB : 45\t\r\nnorm.s1-condA : 26\t\r\nnorm.s2-condA : 28\t\r\nnorm.s3-condB : 28\t\r\nnorm.s4-condB : 29\t\r\nbaseMean : 27.91\t\r\n**condA : 27\t\r\ncondB : 28\t\r\nFoldChange : 1.01\t\r\nlog2FoldChange : 0.015**\t\r\npvalue : 0.885040513937845\t\r\npadj : 0.999879379281527\t\r\ndispGeneEst : 0\t\r\ndispFit : 0.099\t\r\ndispMAP : 0.083\t\r\ndispersion : 0.083\t\r\nbetaConv : TRUE\t\r\nmaxCooks : NA\r\n\r\nMy condition of reference is condA.\r\n\r\nIf I'm correct, FoldChange = 28/27= 1,037037037 --> around to 1.04. Here we have 1.01 instead.\r\nAnd log2FoldChange = log2(1,037037037) = 0,052467 --> around to 0.052. Here we have 0.015 instead.\r\n\r\nI want to know if there's an explanation for this inconsistency. Because if there's an error, so pvalue and padj could be questioned too...\r\n\r\nThanks,\r\nAlexandra"},"comment":{"url":"https://api.github.com/repos/PF2-pasteur-fr/SARTools/issues/comments/237847376","html_url":"https://github.com/PF2-pasteur-fr/SARTools/issues/20#issuecomment-237847376","issue_url":"https://api.github.com/repos/PF2-pasteur-fr/SARTools/issues/20","id":237847376,"user":{"login":"AlexandraBomane","id":9327758,"avatar_url":"https://avatars.githubusercontent.com/u/9327758?v=3","gravatar_id":"","url":"https://api.github.com/users/AlexandraBomane","html_url":"https://github.com/AlexandraBomane","followers_url":"https://api.github.com/users/AlexandraBomane/followers","following_url":"https://api.github.com/users/AlexandraBomane/following{/other_user}","gists_url":"https://api.github.com/users/AlexandraBomane/gists{/gist_id}","starred_url":"https://api.github.com/users/AlexandraBomane/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/AlexandraBomane/subscriptions","organizations_url":"https://api.github.com/users/AlexandraBomane/orgs","repos_url":"https://api.github.com/users/AlexandraBomane/repos","events_url":"https://api.github.com/users/AlexandraBomane/events{/privacy}","received_events_url":"https://api.github.com/users/AlexandraBomane/received_events","type":"User","site_admin":false},"created_at":"2016-08-05T13:16:33Z","updated_at":"2016-08-05T13:16:33Z","body":"Is it possible to disable the shrinkage in SARTools ?\r\n\r\nThanks,\r\nAlexandra"}}
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