{"action":"created","issue":{"url":"https://api.github.com/repos/yanwu2014/swne/issues/6","repository_url":"https://api.github.com/repos/yanwu2014/swne","labels_url":"https://api.github.com/repos/yanwu2014/swne/issues/6/labels{/name}","comments_url":"https://api.github.com/repos/yanwu2014/swne/issues/6/comments","events_url":"https://api.github.com/repos/yanwu2014/swne/issues/6/events","html_url":"https://github.com/yanwu2014/swne/issues/6","id":348430500,"node_id":"MDU6SXNzdWUzNDg0MzA1MDA=","number":6,"title":"primary steps uploading seurat object","user":{"login":"mooreann","id":32822978,"node_id":"MDQ6VXNlcjMyODIyOTc4","avatar_url":"https://avatars0.githubusercontent.com/u/32822978?v=4","gravatar_id":"","url":"https://api.github.com/users/mooreann","html_url":"https://github.com/mooreann","followers_url":"https://api.github.com/users/mooreann/followers","following_url":"https://api.github.com/users/mooreann/following{/other_user}","gists_url":"https://api.github.com/users/mooreann/gists{/gist_id}","starred_url":"https://api.github.com/users/mooreann/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mooreann/subscriptions","organizations_url":"https://api.github.com/users/mooreann/orgs","repos_url":"https://api.github.com/users/mooreann/repos","events_url":"https://api.github.com/users/mooreann/events{/privacy}","received_events_url":"https://api.github.com/users/mooreann/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":8,"created_at":"2018-08-07T18:10:22Z","updated_at":"2018-08-15T21:32:58Z","closed_at":null,"author_association":"NONE","body":"I'm trying to filter the data of my Seurat matrix and extract the norm counts based off the posted walk through. First I was wondering how necessary it is to filter given my imported object was already filtered in Seurat.\r\nMy bigger question though, is that both the filtering and extracting norm counts seem to require the raw data of the object to be an S4 object of dgCMatrix class.\r\nThe current object I'm trying to use has the data in this format, but the raw data is still an S3 data frame. Is there any way to get around this or is there a way to reformat the raw data within the object?"},"comment":{"url":"https://api.github.com/repos/yanwu2014/swne/issues/comments/413344684","html_url":"https://github.com/yanwu2014/swne/issues/6#issuecomment-413344684","issue_url":"https://api.github.com/repos/yanwu2014/swne/issues/6","id":413344684,"node_id":"MDEyOklzc3VlQ29tbWVudDQxMzM0NDY4NA==","user":{"login":"yanwu2014","id":1645621,"node_id":"MDQ6VXNlcjE2NDU2MjE=","avatar_url":"https://avatars1.githubusercontent.com/u/1645621?v=4","gravatar_id":"","url":"https://api.github.com/users/yanwu2014","html_url":"https://github.com/yanwu2014","followers_url":"https://api.github.com/users/yanwu2014/followers","following_url":"https://api.github.com/users/yanwu2014/following{/other_user}","gists_url":"https://api.github.com/users/yanwu2014/gists{/gist_id}","starred_url":"https://api.github.com/users/yanwu2014/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/yanwu2014/subscriptions","organizations_url":"https://api.github.com/users/yanwu2014/orgs","repos_url":"https://api.github.com/users/yanwu2014/repos","events_url":"https://api.github.com/users/yanwu2014/events{/privacy}","received_events_url":"https://api.github.com/users/yanwu2014/received_events","type":"User","site_admin":false},"created_at":"2018-08-15T21:32:58Z","updated_at":"2018-08-15T21:32:58Z","author_association":"OWNER","body":"Ah can you update SWNE? We've made it so that there's only one line, and you're looking for the `k` when that line first crosses zero. We've also changed it back so that the output of `FindNumFactors` returns a list again, and one of the list elements is the optimal `k`\r\n\r\nThe line refers to the error reduction above noise. So every time we increase the value of `k`, we look at the decrease reconstruction error for your input matrix, and then the decrease in reconstruction error for a randomized input matrix. Once the decrease in reconstruction error for the input matrix falls below the decrease in reconstruction error for the randomized matrix, there's no more benefit to increasing `k` so we keep that value of `k`. Sorry I know this can be a little confusing. \r\n\r\nLet me know if you have any more questions! "}}
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