{"action":"created","issue":{"url":"https://api.github.com/repos/evoreprice/lmdPaper/issues/9","labels_url":"https://api.github.com/repos/evoreprice/lmdPaper/issues/9/labels{/name}","comments_url":"https://api.github.com/repos/evoreprice/lmdPaper/issues/9/comments","events_url":"https://api.github.com/repos/evoreprice/lmdPaper/issues/9/events","html_url":"https://github.com/evoreprice/lmdPaper/issues/9","id":108300038,"number":9,"title":"Magnitude of LFCs in f_madsTree","user":{"login":"TomHarrop","id":5971975,"avatar_url":"https://avatars.githubusercontent.com/u/5971975?v=3","gravatar_id":"","url":"https://api.github.com/users/TomHarrop","html_url":"https://github.com/TomHarrop","followers_url":"https://api.github.com/users/TomHarrop/followers","following_url":"https://api.github.com/users/TomHarrop/following{/other_user}","gists_url":"https://api.github.com/users/TomHarrop/gists{/gist_id}","starred_url":"https://api.github.com/users/TomHarrop/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/TomHarrop/subscriptions","organizations_url":"https://api.github.com/users/TomHarrop/orgs","repos_url":"https://api.github.com/users/TomHarrop/repos","events_url":"https://api.github.com/users/TomHarrop/events{/privacy}","received_events_url":"https://api.github.com/users/TomHarrop/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"TomHarrop","id":5971975,"avatar_url":"https://avatars.githubusercontent.com/u/5971975?v=3","gravatar_id":"","url":"https://api.github.com/users/TomHarrop","html_url":"https://github.com/TomHarrop","followers_url":"https://api.github.com/users/TomHarrop/followers","following_url":"https://api.github.com/users/TomHarrop/following{/other_user}","gists_url":"https://api.github.com/users/TomHarrop/gists{/gist_id}","starred_url":"https://api.github.com/users/TomHarrop/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/TomHarrop/subscriptions","organizations_url":"https://api.github.com/users/TomHarrop/orgs","repos_url":"https://api.github.com/users/TomHarrop/repos","events_url":"https://api.github.com/users/TomHarrop/events{/privacy}","received_events_url":"https://api.github.com/users/TomHarrop/received_events","type":"User","site_admin":false},"milestone":null,"comments":1,"created_at":"2015-09-25T10:19:18Z","updated_at":"2015-09-25T14:44:46Z","closed_at":null,"body":"At the moment extremely lowly-expressed genes will still be given a colour in the figure. Could remove is.na(padj)?"},"comment":{"url":"https://api.github.com/repos/evoreprice/lmdPaper/issues/comments/143242195","html_url":"https://github.com/evoreprice/lmdPaper/issues/9#issuecomment-143242195","issue_url":"https://api.github.com/repos/evoreprice/lmdPaper/issues/9","id":143242195,"user":{"login":"TomHarrop","id":5971975,"avatar_url":"https://avatars.githubusercontent.com/u/5971975?v=3","gravatar_id":"","url":"https://api.github.com/users/TomHarrop","html_url":"https://github.com/TomHarrop","followers_url":"https://api.github.com/users/TomHarrop/followers","following_url":"https://api.github.com/users/TomHarrop/following{/other_user}","gists_url":"https://api.github.com/users/TomHarrop/gists{/gist_id}","starred_url":"https://api.github.com/users/TomHarrop/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/TomHarrop/subscriptions","organizations_url":"https://api.github.com/users/TomHarrop/orgs","repos_url":"https://api.github.com/users/TomHarrop/repos","events_url":"https://api.github.com/users/TomHarrop/events{/privacy}","received_events_url":"https://api.github.com/users/TomHarrop/received_events","type":"User","site_admin":false},"created_at":"2015-09-25T14:44:46Z","updated_at":"2015-09-25T14:44:46Z","body":"### Should I set a threshold on the LFC?\r\n\r\nThis will affect the number of genes that get `padj = NA`.\r\n\r\nDon't know if it will affect the number of MADS genes; maybe for tomato?\r\n\r\n* `padj == NA` means either:\r\n    * all samples have zero counts\r\n    * there was an extreme outlier\r\n    * the row was filtered by automatic filtering (based on low mean normalized count)\r\n\r\n### Should I set an `alpha` threshold?\r\n\r\n* automatic filtering is based on `alpha`. Lower `alpha` should mean more `NA`s.\r\n    * for the rice dataset it seems like lowering `alpha` from 0.1 to 0.01 rejects an additional 1,824 genes\r\n\r\n### Check the number rejected from automatic filtering\r\n`dim(res[is.na(padj) & !is.na(pvalue)])[1]`\r\n* for default settings (`lfcThreshold = 0`, `alpha = 0.1`): it's 14,592\r\n* `lfcThreshold = 1`: 18,240\r\n* `alpha = 0.01`: 16,416\r\n* `alpha = 0.01`, `lfcThreshold = 1`: 20,064\r\n"}}