{"action":"created","issue":{"url":"https://api.github.com/repos/RobertsLab/resources/issues/762","repository_url":"https://api.github.com/repos/RobertsLab/resources","labels_url":"https://api.github.com/repos/RobertsLab/resources/issues/762/labels{/name}","comments_url":"https://api.github.com/repos/RobertsLab/resources/issues/762/comments","events_url":"https://api.github.com/repos/RobertsLab/resources/issues/762/events","html_url":"https://github.com/RobertsLab/resources/issues/762","id":504284991,"node_id":"MDU6SXNzdWU1MDQyODQ5OTE=","number":762,"title":"Questions about MethylKit parameters for C. gigas","user":{"login":"RoeArEs","id":44410680,"node_id":"MDQ6VXNlcjQ0NDEwNjgw","avatar_url":"https://avatars3.githubusercontent.com/u/44410680?v=4","gravatar_id":"","url":"https://api.github.com/users/RoeArEs","html_url":"https://github.com/RoeArEs","followers_url":"https://api.github.com/users/RoeArEs/followers","following_url":"https://api.github.com/users/RoeArEs/following{/other_user}","gists_url":"https://api.github.com/users/RoeArEs/gists{/gist_id}","starred_url":"https://api.github.com/users/RoeArEs/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/RoeArEs/subscriptions","organizations_url":"https://api.github.com/users/RoeArEs/orgs","repos_url":"https://api.github.com/users/RoeArEs/repos","events_url":"https://api.github.com/users/RoeArEs/events{/privacy}","received_events_url":"https://api.github.com/users/RoeArEs/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":{"login":"yaaminiv","id":22335838,"node_id":"MDQ6VXNlcjIyMzM1ODM4","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},"assignees":[{"login":"yaaminiv","id":22335838,"node_id":"MDQ6VXNlcjIyMzM1ODM4","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}],"milestone":null,"comments":1,"created_at":"2019-10-08T21:18:32Z","updated_at":"2019-10-09T20:01:43Z","closed_at":null,"author_association":"NONE","body":"Hello everybudy. I have a couple questions about MethylKit. Here I go...\r\n\r\nIn context of samples ID's I have:\r\nThermal-susceptible families (3 replicates per family): \r\nFamily 05 = 0501, 0502 and 0503\r\nFamily 35 = 3501, 3502 and 3503\r\nThermal-resistant families:\r\nFamily 52 = 5201, 5202 and 5203\r\nFamily 59 = 5901, 5902 and 5903\r\n\r\n1: The output results from group of samples analysis is different than phenotypes analysis.\r\nIn group of samples I have the considerations like:\r\n## Samples IDS\r\nsample_ids_list <- list(\"0501\", \"0502\", \"0503\", \r\n                                   \"3501\", \"3502\", \"3503\",\r\n                                   \"5201\", \"5202\", \"5203\", \r\n                                   \"5901\", \"5902\", \"5903\")\r\nAfet, I used this assignation:\r\nSet number of families 05, 35, 52 or 59 treatments.\r\n0, 1, 2  3 is assigned to each sample ID corresponding to a particular treatment.\r\ntreatmentSpecification <- c(rep(0, times = 3), rep(1, times = 3), rep(2, times=3), rep(3, times=3))\r\n\r\nThis is the specification for families but NOT for phenotypes.\r\nIn this it looks that all will be compared taking the 0 as a reference. At the end I couldn't know where the differential methylation calls belongs. I mean, the difference will be assigned to which family?\r\n\r\nThen I wanted to fix it considering phenotypes (Thermal-susceptible vs thermal-resistant) like:\r\n\r\nSamples IDS\r\nsample_ids_list <- list(\"0501\", \"0502\", \"0503\", \"3501\", \"3502\", \"3503\",\r\n                                   \"5201\", \"5202\", \"5203\",  \"5901\", \"5902\", \"5903\")\r\nSet number of phenotypes TS or TR treatments.\r\n0 or 1 assigned to each phenotype ID corresponding to a particular treatment.\r\ntreatmentSpecification <- c(rep(0, times = 6), rep(1, times = 6))\r\n\r\nHere will be the same, taking 0 as a reference to compare against 1 (where 0 is thermal-susceptible).\r\n\r\n2: In the methylation analysis, the percentage considerer could be 25 or 50. I understand how the result will be but in my case, Is it OK if I preferred 25? It is because I would like to see more data and infer if some DML or DMR are related with my differentially expressed genes between phenotypes in promoters."},"comment":{"url":"https://api.github.com/repos/RobertsLab/resources/issues/comments/540166430","html_url":"https://github.com/RobertsLab/resources/issues/762#issuecomment-540166430","issue_url":"https://api.github.com/repos/RobertsLab/resources/issues/762","id":540166430,"node_id":"MDEyOklzc3VlQ29tbWVudDU0MDE2NjQzMA==","user":{"login":"RoeArEs","id":44410680,"node_id":"MDQ6VXNlcjQ0NDEwNjgw","avatar_url":"https://avatars3.githubusercontent.com/u/44410680?v=4","gravatar_id":"","url":"https://api.github.com/users/RoeArEs","html_url":"https://github.com/RoeArEs","followers_url":"https://api.github.com/users/RoeArEs/followers","following_url":"https://api.github.com/users/RoeArEs/following{/other_user}","gists_url":"https://api.github.com/users/RoeArEs/gists{/gist_id}","starred_url":"https://api.github.com/users/RoeArEs/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/RoeArEs/subscriptions","organizations_url":"https://api.github.com/users/RoeArEs/orgs","repos_url":"https://api.github.com/users/RoeArEs/repos","events_url":"https://api.github.com/users/RoeArEs/events{/privacy}","received_events_url":"https://api.github.com/users/RoeArEs/received_events","type":"User","site_admin":false},"created_at":"2019-10-09T20:01:43Z","updated_at":"2019-10-09T20:01:43Z","author_association":"NONE","body":"Yes, I am on it now. Testing the 25 %. I will let you know the difference. Thanks"}}
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