{"action":"created","issue":{"url":"https://api.github.com/repos/RamsinghLab/arkas/issues/17","repository_url":"https://api.github.com/repos/RamsinghLab/arkas","labels_url":"https://api.github.com/repos/RamsinghLab/arkas/issues/17/labels{/name}","comments_url":"https://api.github.com/repos/RamsinghLab/arkas/issues/17/comments","events_url":"https://api.github.com/repos/RamsinghLab/arkas/issues/17/events","html_url":"https://github.com/RamsinghLab/arkas/issues/17","id":164919452,"number":17,"title":"calcTPM must match tsv file","user":{"login":"arcolombo","id":5473099,"avatar_url":"https://avatars.githubusercontent.com/u/5473099?v=3","gravatar_id":"","url":"https://api.github.com/users/arcolombo","html_url":"https://github.com/arcolombo","followers_url":"https://api.github.com/users/arcolombo/followers","following_url":"https://api.github.com/users/arcolombo/following{/other_user}","gists_url":"https://api.github.com/users/arcolombo/gists{/gist_id}","starred_url":"https://api.github.com/users/arcolombo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/arcolombo/subscriptions","organizations_url":"https://api.github.com/users/arcolombo/orgs","repos_url":"https://api.github.com/users/arcolombo/repos","events_url":"https://api.github.com/users/arcolombo/events{/privacy}","received_events_url":"https://api.github.com/users/arcolombo/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":3,"created_at":"2016-07-11T19:51:49Z","updated_at":"2016-07-11T22:01:16Z","closed_at":null,"body":"need to rwite a test for calcTPM to ensure that the tpm calculation is correct with respect to kallisto versions."},"comment":{"url":"https://api.github.com/repos/RamsinghLab/arkas/issues/comments/231879194","html_url":"https://github.com/RamsinghLab/arkas/issues/17#issuecomment-231879194","issue_url":"https://api.github.com/repos/RamsinghLab/arkas/issues/17","id":231879194,"user":{"login":"ttriche","id":4386,"avatar_url":"https://avatars.githubusercontent.com/u/4386?v=3","gravatar_id":"","url":"https://api.github.com/users/ttriche","html_url":"https://github.com/ttriche","followers_url":"https://api.github.com/users/ttriche/followers","following_url":"https://api.github.com/users/ttriche/following{/other_user}","gists_url":"https://api.github.com/users/ttriche/gists{/gist_id}","starred_url":"https://api.github.com/users/ttriche/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ttriche/subscriptions","organizations_url":"https://api.github.com/users/ttriche/orgs","repos_url":"https://api.github.com/users/ttriche/repos","events_url":"https://api.github.com/users/ttriche/events{/privacy}","received_events_url":"https://api.github.com/users/ttriche/received_events","type":"User","site_admin":false},"created_at":"2016-07-11T22:01:15Z","updated_at":"2016-07-11T22:01:15Z","body":"calcTpm is used to feed the matrix that tpm() pulls from, so those will\nalways be identical.  At some point there was a regression propagated from\nHEAD (RamsinghLab/arkas) into my fork, which had not previously been there,\nand had thrown off the calculations.  It turns out that leaving the TPM\ncalculation to the last minute (i.e., within the KallistoExperiment()\nconstructor) is faster and less error-prone, as is carving out the\ncalculation into its own little function that handles matrices and vectors\n(row/column matrices) directly.  Hence calcTpm.\n\nI spot-checked this on TARGET AML samples locally and I get no differences\ngreater than 0.0001 TPM, which is well within the margin of error due to\nrounding/truncation.  calcTpm also has the benefit of corresponding exactly\n(both variable names and logic) to that which Kallisto performs internally.\n\n\n--t\n\nOn Mon, Jul 11, 2016 at 2:22 PM, Anthony R. Colombo <\nnotifications@github.com> wrote:\n\n> Tpm-Err.pdf\n> <https://github.com/RamsinghLab/arkas/files/358108/Tpm-Err.pdf>\n>\n> this shows the functoin calcTPM versus the generic accessor tpm(), so I'm\n> not sure how @ttriche <https://github.com/ttriche> hit an error.\n> collapseTpm() uses tpm accessor and this plot shows its identical. I'm\n> suspecting it was a version clash.? needs some data to reproduce @triche\n> <https://github.com/triche>'s issue....\n>\n> —\n> You are receiving this because you were mentioned.\n> Reply to this email directly, view it on GitHub\n> <https://github.com/RamsinghLab/arkas/issues/17#issuecomment-231869281>,\n> or mute the thread\n> <https://github.com/notifications/unsubscribe/AAARIspIK7auJHXAT9wr847oaCQSIhw4ks5qUrQNgaJpZM4JJt7g>\n> .\n>\n"}}
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