{"action":"created","issue":{"url":"https://api.github.com/repos/AlexsLemonade/refinebio/issues/232","repository_url":"https://api.github.com/repos/AlexsLemonade/refinebio","labels_url":"https://api.github.com/repos/AlexsLemonade/refinebio/issues/232/labels{/name}","comments_url":"https://api.github.com/repos/AlexsLemonade/refinebio/issues/232/comments","events_url":"https://api.github.com/repos/AlexsLemonade/refinebio/issues/232/events","html_url":"https://github.com/AlexsLemonade/refinebio/issues/232","id":318914999,"number":232,"title":"Add Support for Non-Human Illumina Platforms","user":{"login":"Miserlou","id":139987,"avatar_url":"https://avatars1.githubusercontent.com/u/139987?v=4","gravatar_id":"","url":"https://api.github.com/users/Miserlou","html_url":"https://github.com/Miserlou","followers_url":"https://api.github.com/users/Miserlou/followers","following_url":"https://api.github.com/users/Miserlou/following{/other_user}","gists_url":"https://api.github.com/users/Miserlou/gists{/gist_id}","starred_url":"https://api.github.com/users/Miserlou/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/Miserlou/subscriptions","organizations_url":"https://api.github.com/users/Miserlou/orgs","repos_url":"https://api.github.com/users/Miserlou/repos","events_url":"https://api.github.com/users/Miserlou/events{/privacy}","received_events_url":"https://api.github.com/users/Miserlou/received_events","type":"User","site_admin":false},"labels":[{"id":918327558,"url":"https://api.github.com/repos/AlexsLemonade/refinebio/labels/illumina%20beadchip","name":"illumina beadchip","color":"3c85c1","default":false},{"id":806635296,"url":"https://api.github.com/repos/AlexsLemonade/refinebio/labels/next","name":"next","color":"ededed","default":false},{"id":892675090,"url":"https://api.github.com/repos/AlexsLemonade/refinebio/labels/processor","name":"processor","color":"0c1a7a","default":false}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":{"url":"https://api.github.com/repos/AlexsLemonade/refinebio/milestones/15","html_url":"https://github.com/AlexsLemonade/refinebio/milestone/15","labels_url":"https://api.github.com/repos/AlexsLemonade/refinebio/milestones/15/labels","id":3308531,"number":15,"title":"Get crunch ready!","description":"","creator":{"login":"jaclyn-taroni","id":19534205,"avatar_url":"https://avatars0.githubusercontent.com/u/19534205?v=4","gravatar_id":"","url":"https://api.github.com/users/jaclyn-taroni","html_url":"https://github.com/jaclyn-taroni","followers_url":"https://api.github.com/users/jaclyn-taroni/followers","following_url":"https://api.github.com/users/jaclyn-taroni/following{/other_user}","gists_url":"https://api.github.com/users/jaclyn-taroni/gists{/gist_id}","starred_url":"https://api.github.com/users/jaclyn-taroni/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jaclyn-taroni/subscriptions","organizations_url":"https://api.github.com/users/jaclyn-taroni/orgs","repos_url":"https://api.github.com/users/jaclyn-taroni/repos","events_url":"https://api.github.com/users/jaclyn-taroni/events{/privacy}","received_events_url":"https://api.github.com/users/jaclyn-taroni/received_events","type":"User","site_admin":false},"open_issues":14,"closed_issues":10,"state":"open","created_at":"2018-04-30T12:14:34Z","updated_at":"2018-05-13T19:09:39Z","due_on":"2018-05-11T07:00:00Z","closed_at":null},"comments":4,"created_at":"2018-04-30T14:41:11Z","updated_at":"2018-05-15T20:27:19Z","closed_at":null,"author_association":"COLLABORATOR","body":"### Context\r\n\r\nQuoting @jaclyn-taroni, via https://github.com/AlexsLemonade/refinebio/pull/212#discussion_r184864928:\r\n\r\n```\r\nThis only supports 2 human platforms, Illumina HumanWG-6 v2.0 (i.e., GPL13376) and Illumina HumanHT-12 V4.0 (i.e., GPL10558), using the relevant bioconductor packages at the moment.\r\n\r\nWe'll want to support a broader set of BeadChips. Specifically, there are bioconductor packages for the following additional platforms:\r\n\r\n    illuminaHumanv1.db\r\n    illuminaHumanv3.db\r\n    illuminaMousev1.db\r\n    illuminaMousev1p1.db\r\n    illuminaMousev2.db\r\n    illuminaRatv1.db\r\n\r\nYou also might consider getting the probe objects like so:\r\n\r\nprobeSequenceRef <- lazyeval::lazy_eval(paste0(platform, \".db::\", platform, \"PROBESEQUENCE\"))\r\nprobeQualityRef <- lazyeval::lazy_eval(paste0(platform, \".db::\", platform, \"PROBEQUALITY\"))\r\nprobeGeneRef <-  lazyeval::lazy_eval(paste0(platform, \".db::\", platform, \"ENSEMBLREANNOTATED\"))\r\n\r\n☝️ would also eliminate the need for loading the annotation library (line 356).\r\n```\r\n\r\n### Problem or idea\r\n\r\nUntil we explicitly add support for other platforms, we'll only be able to process results from two human Illumina platforms. \r\n\r\n### Solution or next step\r\n\r\nJackie has also ready described the solution, so I think it just needs to be implemented. There may be a little bit of work to detect the platform as well.\r\n\r\n### New Issue Checklist\r\n\r\n- [x] The title is short and descriptive.\r\n- [x] You have explained the context that led you to write this issue.\r\n- [x] You have reported a problem or idea.\r\n- [x] You have proposed a solution or next step.\r\n"},"comment":{"url":"https://api.github.com/repos/AlexsLemonade/refinebio/issues/comments/389302061","html_url":"https://github.com/AlexsLemonade/refinebio/issues/232#issuecomment-389302061","issue_url":"https://api.github.com/repos/AlexsLemonade/refinebio/issues/232","id":389302061,"user":{"login":"jaclyn-taroni","id":19534205,"avatar_url":"https://avatars0.githubusercontent.com/u/19534205?v=4","gravatar_id":"","url":"https://api.github.com/users/jaclyn-taroni","html_url":"https://github.com/jaclyn-taroni","followers_url":"https://api.github.com/users/jaclyn-taroni/followers","following_url":"https://api.github.com/users/jaclyn-taroni/following{/other_user}","gists_url":"https://api.github.com/users/jaclyn-taroni/gists{/gist_id}","starred_url":"https://api.github.com/users/jaclyn-taroni/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jaclyn-taroni/subscriptions","organizations_url":"https://api.github.com/users/jaclyn-taroni/orgs","repos_url":"https://api.github.com/users/jaclyn-taroni/repos","events_url":"https://api.github.com/users/jaclyn-taroni/events{/privacy}","received_events_url":"https://api.github.com/users/jaclyn-taroni/received_events","type":"User","site_admin":false},"created_at":"2018-05-15T20:27:19Z","updated_at":"2018-05-15T20:27:19Z","author_association":"NONE","body":"I've just gone through the human platforms. Here's a Bioconductor package to platform name mapping that I think should work:\r\n\r\n`illuminaHumanv1.db`: Illumina Human-6 v1.0, Illumina HumanRef-8 v1.0\r\n`illuminaHumanv2.db`: Illumina Human-6 V2.0, Illumina HumanRef-8 v2.0\r\n`illuminaHumanv3.db`: Illumina HumanHT-12 V3.0, Illumina HumanRef-8 v3.0, Illumina HumanWG-6 V3.0\r\n`illuminaHumanv4.db`: Illumina HumanHT-12 V4.0\r\n\r\nI'm thinking we might want to be a bit more stringent here:\r\nhttps://github.com/AlexsLemonade/refinebio/blob/dev/workers/data_refinery_workers/processors/illumina.R#L414\r\n\r\nSpecifically, we might want some (high) percentage of the expression data probes and the probes from the packages to overlap and for the processing to fail if they don't (i.e., move that check to before the SCAN norm parts that are more intensive).\r\n"}}
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