{"action":"created","issue":{"url":"https://api.github.com/repos/taoliu/MACS/issues/90","labels_url":"https://api.github.com/repos/taoliu/MACS/issues/90/labels{/name}","comments_url":"https://api.github.com/repos/taoliu/MACS/issues/90/comments","events_url":"https://api.github.com/repos/taoliu/MACS/issues/90/events","html_url":"https://github.com/taoliu/MACS/issues/90","id":98247581,"number":90,"title":"control lambda bedGraph","user":{"login":"igordot","id":6363505,"avatar_url":"https://avatars.githubusercontent.com/u/6363505?v=3","gravatar_id":"","url":"https://api.github.com/users/igordot","html_url":"https://github.com/igordot","followers_url":"https://api.github.com/users/igordot/followers","following_url":"https://api.github.com/users/igordot/following{/other_user}","gists_url":"https://api.github.com/users/igordot/gists{/gist_id}","starred_url":"https://api.github.com/users/igordot/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/igordot/subscriptions","organizations_url":"https://api.github.com/users/igordot/orgs","repos_url":"https://api.github.com/users/igordot/repos","events_url":"https://api.github.com/users/igordot/events{/privacy}","received_events_url":"https://api.github.com/users/igordot/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2015-07-30T19:47:25Z","updated_at":"2015-07-30T20:34:52Z","closed_at":"2015-07-30T20:06:02Z","body":"The best description of lambda I could find (https://groups.google.com/forum/#!msg/macs-announcement/JkufzGpUNRk/kUx0z2M2b_cJ):\r\n> For each peak region, MACS calculates the a local lambda for poisson\r\n> distribution based on the control tags within the 1kb, 5kb and\r\n> 10kb(1/5/10k are parameters that you can modify) nearby regions to\r\n> consider the local fluctuations and biases. The local lambda is the\r\n> maximum of the averages of tags for 1/5/10 kb regions and a whole\r\n> genome background. Then this local lambda is used to calculate the p-\r\n> value of poisson distribution.\r\n\r\nWith the --bdg parameter, I can output control_lambda.bdg files. If lambda is calculated locally, how is that translated into bedGraph peaks or are those showing something else entirely? Also, if lambda is calculated around peak regions, shouldn't most of the genome not have any values then?\r\n"},"comment":{"url":"https://api.github.com/repos/taoliu/MACS/issues/comments/126476208","html_url":"https://github.com/taoliu/MACS/issues/90#issuecomment-126476208","issue_url":"https://api.github.com/repos/taoliu/MACS/issues/90","id":126476208,"user":{"login":"igordot","id":6363505,"avatar_url":"https://avatars.githubusercontent.com/u/6363505?v=3","gravatar_id":"","url":"https://api.github.com/users/igordot","html_url":"https://github.com/igordot","followers_url":"https://api.github.com/users/igordot/followers","following_url":"https://api.github.com/users/igordot/following{/other_user}","gists_url":"https://api.github.com/users/igordot/gists{/gist_id}","starred_url":"https://api.github.com/users/igordot/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/igordot/subscriptions","organizations_url":"https://api.github.com/users/igordot/orgs","repos_url":"https://api.github.com/users/igordot/repos","events_url":"https://api.github.com/users/igordot/events{/privacy}","received_events_url":"https://api.github.com/users/igordot/received_events","type":"User","site_admin":false},"created_at":"2015-07-30T20:34:52Z","updated_at":"2015-07-30T20:34:52Z","body":"All my samples are roughly even in terms of reads. They all have over 15M reads, even after duplicate removal, which should be sufficient. Even before worrying about treatment samples, why do the lambda pileups differ even though the inputs look similar? Treatment samples should not affect that, right?"}}