{"action":"created","issue":{"url":"https://api.github.com/repos/RobertsLab/resources/issues/50","repository_url":"https://api.github.com/repos/RobertsLab/resources","labels_url":"https://api.github.com/repos/RobertsLab/resources/issues/50/labels{/name}","comments_url":"https://api.github.com/repos/RobertsLab/resources/issues/50/comments","events_url":"https://api.github.com/repos/RobertsLab/resources/issues/50/events","html_url":"https://github.com/RobertsLab/resources/issues/50","id":256544202,"number":50,"title":"difficulty with technical replicate clustering","user":{"login":"yaaminiv","id":22335838,"avatar_url":"https://avatars0.githubusercontent.com/u/22335838?v=4","gravatar_id":"","url":"https://api.github.com/users/yaaminiv","html_url":"https://github.com/yaaminiv","followers_url":"https://api.github.com/users/yaaminiv/followers","following_url":"https://api.github.com/users/yaaminiv/following{/other_user}","gists_url":"https://api.github.com/users/yaaminiv/gists{/gist_id}","starred_url":"https://api.github.com/users/yaaminiv/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yaaminiv/subscriptions","organizations_url":"https://api.github.com/users/yaaminiv/orgs","repos_url":"https://api.github.com/users/yaaminiv/repos","events_url":"https://api.github.com/users/yaaminiv/events{/privacy}","received_events_url":"https://api.github.com/users/yaaminiv/received_events","type":"User","site_admin":false},"labels":[{"id":664409261,"url":"https://api.github.com/repos/RobertsLab/resources/labels/question","name":"question","color":"cc317c","default":true}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2017-09-10T22:10:29Z","updated_at":"2017-09-11T00:32:54Z","closed_at":null,"author_association":"NONE","body":"In the first step of my analysis, I made an NMDS plot using euclidean distances to see if my technical replicates (two separate injections on the mass spectrometer) clustered well. Unfortunately it's a bit of a...shit show. I've gone through my [R code](https://github.com/RobertsLab/project-oyster-oa/blob/master/analyses/DNR_SRM_20170902/2017-09-06-NMDS-for-Technical-Replication.R) a few times to see if I made any mistakes reading in data, but I don't think I can find any. This is the best technical replicate clustering I have (I use the term \"best\" loosely):\r\n\r\n![nmds](https://raw.githubusercontent.com/RobertsLab/project-oyster-oa/master/analyses/DNR_SRM_20170902/2017-09-08-NMDS-TechnicalReplication-Normalized.jpeg)\r\n\r\nThe distances between ordinations for each technical replicate is visualized below:\r\n\r\n![distances](https://raw.githubusercontent.com/RobertsLab/project-oyster-oa/master/analyses/DNR_SRM_20170902/2017-09-08-NMDS-TechnicalReplication-Ordination-Distances.jpeg)\r\n\r\nI'd appreciate if anyone could 1) give my code a look and see if they catch any mistakes I made or 2) give me advice on how to best explain this mishap in my PCSGA presentation!\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/RobertsLab/resources/issues/comments/328386630","html_url":"https://github.com/RobertsLab/resources/issues/50#issuecomment-328386630","issue_url":"https://api.github.com/repos/RobertsLab/resources/issues/50","id":328386630,"user":{"login":"sr320","id":4442039,"avatar_url":"https://avatars1.githubusercontent.com/u/4442039?v=4","gravatar_id":"","url":"https://api.github.com/users/sr320","html_url":"https://github.com/sr320","followers_url":"https://api.github.com/users/sr320/followers","following_url":"https://api.github.com/users/sr320/following{/other_user}","gists_url":"https://api.github.com/users/sr320/gists{/gist_id}","starred_url":"https://api.github.com/users/sr320/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sr320/subscriptions","organizations_url":"https://api.github.com/users/sr320/orgs","repos_url":"https://api.github.com/users/sr320/repos","events_url":"https://api.github.com/users/sr320/events{/privacy}","received_events_url":"https://api.github.com/users/sr320/received_events","type":"User","site_admin":false},"created_at":"2017-09-11T00:32:54Z","updated_at":"2017-09-11T00:32:54Z","author_association":"CONTRIBUTOR","body":"Also - go ahead make protein specific graphs with averages of technical replicates."}}
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