{"action":"created","comment":{"url":"https://api.github.com/repos/AlexsLemonade/refinebio-docs/pulls/comments/350281776","pull_request_review_id":322400533,"id":350281776,"node_id":"MDI0OlB1bGxSZXF1ZXN0UmV2aWV3Q29tbWVudDM1MDI4MTc3Ng==","diff_hunk":"@@ -437,7 +437,15 @@ We then quantile normalize all samples as described above.\n \n We've made our analyses underlying processing choices and exploring test compendia available at our <a href = \"https://github.com/AlexsLemonade/compendium-processing\" target = \"blank\">`compendium-processing`</a> repository.\n \n-### Download Folder\n+### Collapsing by genus\n+\n+Microarray platforms are generally designed to assay samples from a specific species.\n+In some cases, samples that are not from the species for which a microarray platform is specifically designed for are in publicly available data surveyed by refine.bio (e.g., samples labeled _Bos indicus_ will be run on _Bos taurus_ microarrays or mouse crosses that are not labeled _Mus musculus_ will be run on _Mus musculus_ microarrays). \n+When we encounter this in refine.bio, we will include samples from the species that differs from the platform species when the two species share a genus in the larger species' normalized compendium (e.g., _Bos indicus_ samples run on _Bos taurus_ microarrays are included in the _Bos taurus_ normalized compendium).","path":"docs/main_text.md","position":9,"original_position":9,"commit_id":"840cdb21341498d35df2d960c7e78b5a53d7fb6a","original_commit_id":"840cdb21341498d35df2d960c7e78b5a53d7fb6a","user":{"login":"jashapiro","id":20483,"node_id":"MDQ6VXNlcjIwNDgz","avatar_url":"https://avatars2.githubusercontent.com/u/20483?v=4","gravatar_id":"","url":"https://api.github.com/users/jashapiro","html_url":"https://github.com/jashapiro","followers_url":"https://api.github.com/users/jashapiro/followers","following_url":"https://api.github.com/users/jashapiro/following{/other_user}","gists_url":"https://api.github.com/users/jashapiro/gists{/gist_id}","starred_url":"https://api.github.com/users/jashapiro/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/jashapiro/subscriptions","organizations_url":"https://api.github.com/users/jashapiro/orgs","repos_url":"https://api.github.com/users/jashapiro/repos","events_url":"https://api.github.com/users/jashapiro/events{/privacy}","received_events_url":"https://api.github.com/users/jashapiro/received_events","type":"User","site_admin":false},"body":"```suggestion\r\nWhen we encounter this in refine.bio, we will include samples in a compendium from species that differ from the primary platform species when the two species share a genus (e.g., _Bos indicus_ samples run on _Bos taurus_ microarrays are included in the _Bos taurus_ normalized compendium).\r\n```\r\n\r\nMy change loses the directionality of the the larger species, but I replaced that with \"primary\" which I hope is clear enough?","created_at":"2019-11-25T16:17:08Z","updated_at":"2019-11-25T16:22:47Z","html_url":"https://github.com/AlexsLemonade/refinebio-docs/pull/120#discussion_r350281776","pull_request_url":"https://api.github.com/repos/AlexsLemonade/refinebio-docs/pulls/120","author_association":"NONE","_links":{"self":{"href":"https://api.github.com/repos/AlexsLemonade/refinebio-docs/pulls/comments/350281776"},"html":{"href":"https://github.com/AlexsLemonade/refinebio-docs/pull/120#discussion_r350281776"},"pull_request":{"href":"https://api.github.com/repos/AlexsLemonade/refinebio-docs/pulls/120"}}},"pull_request":{"url":"https://api.github.com/repos/AlexsLemonade/refinebio-docs/pulls/120","id":345282618,"node_id":"MDExOlB1bGxSZXF1ZXN0MzQ1MjgyNjE4","html_url":"https://github.com/AlexsLemonade/refinebio-docs/pull/120","diff_url":"https://github.com/AlexsLemonade/refinebio-docs/pull/120.diff","patch_url":"https://github.com/AlexsLemonade/refinebio-docs/pull/120.patch","issue_url":"https://api.github.com/repos/AlexsLemonade/refinebio-docs/issues/120","number":120,"state":"open","locked":false,"title":"Add note about samples from the same genus in normalized compendia","user":{"login":"jaclyn-taroni","id":19534205,"node_id":"MDQ6VXNlcjE5NTM0MjA1","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},"body":"Closes #116. Is this clear? I found this a bit challenging to write about clearly (and maybe I have not accomplished that).","created_at":"2019-11-25T15:40:26Z","updated_at":"2019-11-25T16:22:46Z","closed_at":null,"merged_at":null,"merge_commit_sha":"2f7c92afdccc37a26405975e1a110d47d3ea3d3d","assignee":null,"assignees":[],"requested_reviewers":[{"login":"davidsmejia","id":1075609,"node_id":"MDQ6VXNlcjEwNzU2MDk=","avatar_url":"https://avatars1.githubusercontent.com/u/1075609?v=4","gravatar_id":"","url":"https://api.github.com/users/davidsmejia","html_url":"https://github.com/davidsmejia","followers_url":"https://api.github.com/users/davidsmejia/followers","following_url":"https://api.github.com/users/davidsmejia/following{/other_user}","gists_url":"https://api.github.com/users/davidsmejia/gists{/gist_id}","starred_url":"https://api.github.com/users/davidsmejia/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/davidsmejia/subscriptions","organizations_url":"https://api.github.com/users/davidsmejia/orgs","repos_url":"https://api.github.com/users/davidsmejia/repos","events_url":"https://api.github.com/users/davidsmejia/events{/privacy}","received_events_url":"https://api.github.com/users/davidsmejia/received_events","type":"User","site_admin":false},{"login":"arielsvn","id":1882507,"node_id":"MDQ6VXNlcjE4ODI1MDc=","avatar_url":"https://avatars1.githubusercontent.com/u/1882507?v=4","gravatar_id":"","url":"https://api.github.com/users/arielsvn","html_url":"https://github.com/arielsvn","followers_url":"https://api.github.com/users/arielsvn/followers","following_url":"https://api.github.com/users/arielsvn/following{/other_user}","gists_url":"https://api.github.com/users/arielsvn/gists{/gist_id}","starred_url":"https://api.github.com/users/arielsvn/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/arielsvn/subscriptions","organizations_url":"https://api.github.com/users/arielsvn/orgs","repos_url":"https://api.github.com/users/arielsvn/repos","events_url":"https://api.github.com/users/arielsvn/events{/privacy}","received_events_url":"https://api.github.com/users/arielsvn/received_events","type":"User","site_admin":false}],"requested_teams":[],"labels":[],"milestone":null,"commits_url":"https://api.github.com/repos/AlexsLemonade/refinebio-docs/pulls/120/commits","review_comments_url":"https://api.github.com/repos/AlexsLemonade/refinebio-docs/pulls/120/comments","review_comment_url":"https://api.github.com/repos/AlexsLemonade/refinebio-docs/pulls/comments{/number}","comments_url":"https://api.github.com/repos/AlexsLemonade/refinebio-docs/issues/120/comments","statuses_url":"https://api.github.com/repos/AlexsLemonade/refinebio-docs/statuses/840cdb21341498d35df2d960c7e78b5a53d7fb6a","head":{"label":"AlexsLemonade:jaclyn-taroni/116-genus","ref":"jaclyn-taroni/116-genus","sha":"840cdb21341498d35df2d960c7e78b5a53d7fb6a","user":{"login":"AlexsLemonade","id":29661525,"node_id":"MDEyOk9yZ2FuaXphdGlvbjI5NjYxNTI1","avatar_url":"https://avatars1.githubusercontent.com/u/29661525?v=4","gravatar_id":"","url":"https://api.github.com/users/AlexsLemonade","html_url":"https://github.com/AlexsLemonade","followers_url":"https://api.github.com/users/AlexsLemonade/followers","following_url":"https://api.github.com/users/AlexsLemonade/following{/other_user}","gists_url":"https://api.github.com/users/AlexsLemonade/gists{/gist_id}","starred_url":"https://api.github.com/users/AlexsLemonade/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/AlexsLemonade/subscriptions","organizations_url":"https://api.github.com/users/AlexsLemonade/orgs","repos_url":"https://api.github.com/users/AlexsLemonade/repos","events_url":"https://api.github.com/users/AlexsLemonade/events{/privacy}","received_events_url":"https://api.github.com/users/AlexsLemonade/received_events","type":"Organization","site_admin":false},"repo":{"id":143775555,"node_id":"MDEwOlJlcG9zaXRvcnkxNDM3NzU1NTU=","name":"refinebio-docs","full_name":"AlexsLemonade/refinebio-docs","private":false,"owner":{"login":"AlexsLemonade","id":29661525,"node_id":"MDEyOk9yZ2FuaXphdGlvbjI5NjYxNTI1","avatar_url":"https://avatars1.githubusercontent.com/u/29661525?v=4","gravatar_id":"","url":"https://api.github.com/users/AlexsLemonade","html_url":"https://github.com/AlexsLemonade","followers_url":"https://api.github.com/users/AlexsLemonade/followers","following_url":"https://api.github.com/users/AlexsLemonade/following{/other_user}","gists_url":"https://api.github.com/users/AlexsLemonade/gists{/gist_id}","starred_url":"https://api.github.com/users/AlexsLemonade/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/AlexsLemonade/subscriptions","organizations_url":"https://api.github.com/users/AlexsLemonade/orgs","repos_url":"https://api.github.com/users/AlexsLemonade/repos","events_url":"https://api.github.com/users/AlexsLemonade/events{/privacy}","received_events_url":"https://api.github.com/users/AlexsLemonade/received_events","type":"Organization","site_admin":false},"html_url":"https://github.com/AlexsLemonade/refinebio-docs","descript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