{"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":2,"created_at":"2018-08-07T18:10:22Z","updated_at":"2018-08-09T02:12:54Z","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/411614646","html_url":"https://github.com/yanwu2014/swne/issues/6#issuecomment-411614646","issue_url":"https://api.github.com/repos/yanwu2014/swne/issues/6","id":411614646,"node_id":"MDEyOklzc3VlQ29tbWVudDQxMTYxNDY0Ng==","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":"2018-08-09T02:12:54Z","updated_at":"2018-08-09T02:12:54Z","author_association":"OWNER","body":"Ah yes this is definitely a flaw with SWNE right now and we're currently working on decreasing the runtime. \r\n\r\nSo the main bottlenecks are the ICA initialization and then NMF, both of which scale very well with the number of columns but can be slow with large amounts of features (rows). I'd imagine 50,000 could take quite a while. I'd suggest using random initialization instead of ICA, which could speed up the runtime by quite a bit. You could also try decreasing the `max.iter` in the `RunNMF` function.\r\n\r\nIf there's any way to do feature selection for your dataset, I'd recommend trying that as well."}}
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