{"action":"created","issue":{"url":"https://api.github.com/repos/your-highness/normR/issues/16","repository_url":"https://api.github.com/repos/your-highness/normR","labels_url":"https://api.github.com/repos/your-highness/normR/issues/16/labels{/name}","comments_url":"https://api.github.com/repos/your-highness/normR/issues/16/comments","events_url":"https://api.github.com/repos/your-highness/normR/issues/16/events","html_url":"https://github.com/your-highness/normR/issues/16","id":334486114,"node_id":"MDU6SXNzdWUzMzQ0ODYxMTQ=","number":16,"title":"interpretion of results","user":{"login":"steffenheyne","id":10652658,"node_id":"MDQ6VXNlcjEwNjUyNjU4","avatar_url":"https://avatars2.githubusercontent.com/u/10652658?v=4","gravatar_id":"","url":"https://api.github.com/users/steffenheyne","html_url":"https://github.com/steffenheyne","followers_url":"https://api.github.com/users/steffenheyne/followers","following_url":"https://api.github.com/users/steffenheyne/following{/other_user}","gists_url":"https://api.github.com/users/steffenheyne/gists{/gist_id}","starred_url":"https://api.github.com/users/steffenheyne/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/steffenheyne/subscriptions","organizations_url":"https://api.github.com/users/steffenheyne/orgs","repos_url":"https://api.github.com/users/steffenheyne/repos","events_url":"https://api.github.com/users/steffenheyne/events{/privacy}","received_events_url":"https://api.github.com/users/steffenheyne/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-06-21T13:09:09Z","updated_at":"2018-06-21T14:23:51Z","closed_at":null,"author_association":"NONE","body":"I want to analyze differential binding of various histone marks and several questions pop up during analysis:\r\n\r\n1. Why diffR() is only using the ChIP, but not the input like enrichR()? Isn't that necessary to capture the right background?\r\n\r\n2. With diffR() I called diffferential peaks/bins. I'm wondering if the skewed class distribution is correct. The first plot highlights the classes on the counts (via getcounts() from the enrichR() model) and the second plot on the normalized enrichments (via getEnrichment()). It looks a bit like the shift between the two conditions is not correctly normalized...(outliers? ) \r\n\r\n![image](https://user-images.githubusercontent.com/10652658/41720536-a78a0f7e-7563-11e8-805c-7e06bc7f875c.png)\r\n\r\n![image](https://user-images.githubusercontent.com/10652658/41720978-edb38e84-7564-11e8-8eef-5e4727404da8.png)\r\n\r\nWhat do you think? Shouldn't the data be \"normalized\" or centered to the cloud where the red \"spike\" in the first plot (count data) is?"},"comment":{"url":"https://api.github.com/repos/your-highness/normR/issues/comments/399121732","html_url":"https://github.com/your-highness/normR/issues/16#issuecomment-399121732","issue_url":"https://api.github.com/repos/your-highness/normR/issues/16","id":399121732,"node_id":"MDEyOklzc3VlQ29tbWVudDM5OTEyMTczMg==","user":{"login":"steffenheyne","id":10652658,"node_id":"MDQ6VXNlcjEwNjUyNjU4","avatar_url":"https://avatars2.githubusercontent.com/u/10652658?v=4","gravatar_id":"","url":"https://api.github.com/users/steffenheyne","html_url":"https://github.com/steffenheyne","followers_url":"https://api.github.com/users/steffenheyne/followers","following_url":"https://api.github.com/users/steffenheyne/following{/other_user}","gists_url":"https://api.github.com/users/steffenheyne/gists{/gist_id}","starred_url":"https://api.github.com/users/steffenheyne/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/steffenheyne/subscriptions","organizations_url":"https://api.github.com/users/steffenheyne/orgs","repos_url":"https://api.github.com/users/steffenheyne/repos","events_url":"https://api.github.com/users/steffenheyne/events{/privacy}","received_events_url":"https://api.github.com/users/steffenheyne/received_events","type":"User","site_admin":false},"created_at":"2018-06-21T14:23:51Z","updated_at":"2018-06-21T14:23:51Z","author_association":"NONE","body":"![image](https://user-images.githubusercontent.com/10652658/41724848-c5ec13bc-756e-11e8-855d-74ef0fba07bf.png)\r\n\r\nah, when I color bins according to the example in the vignette to the enrichR classes, it seems some of the bins with an offset and high counts are identified as background (and I confirmed this myself in IGV for some of these and I see also very high input enrichment in those bins!)\r\n\r\nbut diffR() seems to use these as there is no input used, or?"}}
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