{"action":"created","issue":{"url":"https://api.github.com/repos/edroaldo/cellrouter/issues/8","repository_url":"https://api.github.com/repos/edroaldo/cellrouter","labels_url":"https://api.github.com/repos/edroaldo/cellrouter/issues/8/labels{/name}","comments_url":"https://api.github.com/repos/edroaldo/cellrouter/issues/8/comments","events_url":"https://api.github.com/repos/edroaldo/cellrouter/issues/8/events","html_url":"https://github.com/edroaldo/cellrouter/issues/8","id":316261393,"number":8,"title":"pretty low GRN scores obtained","user":{"login":"JianmeiZhong","id":37535747,"avatar_url":"https://avatars2.githubusercontent.com/u/37535747?v=4","gravatar_id":"","url":"https://api.github.com/users/JianmeiZhong","html_url":"https://github.com/JianmeiZhong","followers_url":"https://api.github.com/users/JianmeiZhong/followers","following_url":"https://api.github.com/users/JianmeiZhong/following{/other_user}","gists_url":"https://api.github.com/users/JianmeiZhong/gists{/gist_id}","starred_url":"https://api.github.com/users/JianmeiZhong/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/JianmeiZhong/subscriptions","organizations_url":"https://api.github.com/users/JianmeiZhong/orgs","repos_url":"https://api.github.com/users/JianmeiZhong/repos","events_url":"https://api.github.com/users/JianmeiZhong/events{/privacy}","received_events_url":"https://api.github.com/users/JianmeiZhong/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":7,"created_at":"2018-04-20T13:10:22Z","updated_at":"2018-04-24T11:44:30Z","closed_at":null,"author_association":"NONE","body":"Hi,\r\n       I work through most part of the analysis pipeline but the results of GRN scores obtained via grnscores() in specified paths SP_10.SP_8 as tSNE and barplot shows.the grn scores have different levels compared to yours presented in several exemplary analysis,that's  level of 0.0* versus 0.* .Sometimes,the GRNscores plot has one or two genes with low scores in both directions.I don't know if there's some wrong configuration in my pipeline.If my source and endpoints are correct and reliable,low scores level are possible for some datasets and it's available?\r\n![barplot](https://user-images.githubusercontent.com/37535747/39050789-438495c2-44d9-11e8-97ba-bd6a4ea498d0.png)\r\nanother questions asking for your guide :)\r\n      known knowledge this project based on are less subpopulations and increasing number of cells along differentiation process.So,k=120 was set according to my understanding in function buildGRN() and creatKNN() to obtain relatively less subpopulations as tSNE plot shows.k value is different a lot from yours.It might be  a cause of low GRN scores?And if a path didn't go through every subpopulation in non-branched cells differentiation,gene expression dynamics with this path can represent entire process of changes?\r\n![tsne](https://user-images.githubusercontent.com/37535747/39050778-385bd228-44d9-11e8-9e05-571bf8013e36.jpg)\r\n\r\nThank a lot !\r\n\r\nJm Zhong\r\n\r\n\r\n\r\n"},"comment":{"url":"https://api.github.com/repos/edroaldo/cellrouter/issues/comments/383901169","html_url":"https://github.com/edroaldo/cellrouter/issues/8#issuecomment-383901169","issue_url":"https://api.github.com/repos/edroaldo/cellrouter/issues/8","id":383901169,"user":{"login":"edroaldo","id":10130503,"avatar_url":"https://avatars3.githubusercontent.com/u/10130503?v=4","gravatar_id":"","url":"https://api.github.com/users/edroaldo","html_url":"https://github.com/edroaldo","followers_url":"https://api.github.com/users/edroaldo/followers","following_url":"https://api.github.com/users/edroaldo/following{/other_user}","gists_url":"https://api.github.com/users/edroaldo/gists{/gist_id}","starred_url":"https://api.github.com/users/edroaldo/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/edroaldo/subscriptions","organizations_url":"https://api.github.com/users/edroaldo/orgs","repos_url":"https://api.github.com/users/edroaldo/repos","events_url":"https://api.github.com/users/edroaldo/events{/privacy}","received_events_url":"https://api.github.com/users/edroaldo/received_events","type":"User","site_admin":false},"created_at":"2018-04-24T11:44:30Z","updated_at":"2018-04-24T11:44:30Z","author_association":"OWNER","body":"Also, would you mind to show me the commands you are using to generate\nthese plots. Just want to double check how your defining the cutoffs...\n\nThanks!\n\nOn Tue, Apr 24, 2018, 7:42 AM Edroaldo Lummertz da Rocha <edroaldo@gmail.com>\nwrote:\n\n> How many genes are you using for GRN reconstruction? I noticed that, for\n> some datasets, a larger GRN produces more interesting results  because each\n> regulator has more target genes. If you have enough memory, you can do it\n> using all genes. If not, you can select more genes from the pca analysis at\n> the top of your script to have more genes in the genes2use variable.\n>\n> Let me know if you decide to try it.\n>\n> Thanks!\n>\n> On Mon, Apr 23, 2018, 1:03 PM JianmeiZhong <notifications@github.com>\n> wrote:\n>\n>> I tried neigh=2 in another sample,nothing seems changed.\n>> [image: sample2]\n>> <https://user-images.githubusercontent.com/37535747/39141763-466ab774-475b-11e8-920f-97ce4143a0b1.png>\n>>\n>> —\n>> You are receiving this because you commented.\n>> Reply to this email directly, view it on GitHub\n>> <https://github.com/edroaldo/cellrouter/issues/8#issuecomment-383648768>,\n>> or mute the thread\n>> <https://github.com/notifications/unsubscribe-auth/AJqUR5HAwFz1cgHtNcQiQUSfuEhRf-D3ks5trgligaJpZM4Tdb6B>\n>> .\n>>\n>\n"}}
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