{"action":"created","issue":{"url":"https://api.github.com/repos/STAT540-UBC/Discussion/issues/247","repository_url":"https://api.github.com/repos/STAT540-UBC/Discussion","labels_url":"https://api.github.com/repos/STAT540-UBC/Discussion/issues/247/labels{/name}","comments_url":"https://api.github.com/repos/STAT540-UBC/Discussion/issues/247/comments","events_url":"https://api.github.com/repos/STAT540-UBC/Discussion/issues/247/events","html_url":"https://github.com/STAT540-UBC/Discussion/issues/247","id":306305287,"number":247,"title":"Assignment 2 Question 5","user":{"login":"missleung","id":22033340,"avatar_url":"https://avatars3.githubusercontent.com/u/22033340?v=4","gravatar_id":"","url":"https://api.github.com/users/missleung","html_url":"https://github.com/missleung","followers_url":"https://api.github.com/users/missleung/followers","following_url":"https://api.github.com/users/missleung/following{/other_user}","gists_url":"https://api.github.com/users/missleung/gists{/gist_id}","starred_url":"https://api.github.com/users/missleung/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/missleung/subscriptions","organizations_url":"https://api.github.com/users/missleung/orgs","repos_url":"https://api.github.com/users/missleung/repos","events_url":"https://api.github.com/users/missleung/events{/privacy}","received_events_url":"https://api.github.com/users/missleung/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":5,"created_at":"2018-03-19T01:14:49Z","updated_at":"2018-03-21T00:02:33Z","closed_at":null,"author_association":"NONE","body":"I'm a little confused on three parts of the question:\r\n\r\n_1. \"Although an FDR cutoff of 0.05 was used, many of the identified genes have smaller FDRs. By taking an average of the FDR across the set of differentially expressed genes, determine the number of genes that we expect to be false discoveries on average.\"_\r\n\r\nTaking the average of the FDR values is simple enough, but I'm not sure how it relates to the number of genes expected to be false discoveries...how do these two relate each other?\r\n\r\n_2. \"Take the top 50 genes differentially expressed by age and create a heatmap of their expression levels in logCPM. Sort the genes by p-values and group the samples by time point.\"_\r\n\r\nAre we looking at the same model or producing another simple linear regression with age as the only variable? Also, do we use the data set after using \"voom()\", or use the original data set and apply log() transformation to it?\r\n\r\n_3. \"Plot the top three genes with the most significant interaction term. Make a scatterplot with log CPM on the y-axis and age on the x-axis. The shape of each point should correspond to the organism part, and the cell type should correspond to the colour. Note: some conditions have multiple samples, so it is best to plot the mean expression of each treatment group\"_\r\n\r\nSo which values are we plotting? At first I thought it was the log CPM gene expression, but it seems that we are looking at the mean gene expression of each treatment group. How do we plot the mean of each treatment group by age? I'm quite lost on this one."},"comment":{"url":"https://api.github.com/repos/STAT540-UBC/Discussion/issues/comments/374798179","html_url":"https://github.com/STAT540-UBC/Discussion/issues/247#issuecomment-374798179","issue_url":"https://api.github.com/repos/STAT540-UBC/Discussion/issues/247","id":374798179,"user":{"login":"oganm","id":6352379,"avatar_url":"https://avatars1.githubusercontent.com/u/6352379?v=4","gravatar_id":"","url":"https://api.github.com/users/oganm","html_url":"https://github.com/oganm","followers_url":"https://api.github.com/users/oganm/followers","following_url":"https://api.github.com/users/oganm/following{/other_user}","gists_url":"https://api.github.com/users/oganm/gists{/gist_id}","starred_url":"https://api.github.com/users/oganm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/oganm/subscriptions","organizations_url":"https://api.github.com/users/oganm/orgs","repos_url":"https://api.github.com/users/oganm/repos","events_url":"https://api.github.com/users/oganm/events{/privacy}","received_events_url":"https://api.github.com/users/oganm/received_events","type":"User","site_admin":false},"created_at":"2018-03-21T00:02:33Z","updated_at":"2018-03-21T00:02:33Z","author_association":"OWNER","body":"Just do what emma said. \r\n\r\n> Related to the role of FDR: by definition, the false discovery rate gives (FDR) gives you the percentage of genes you expect to be false positives. So if a group of genes has an FDR of 0.05, we would expect on average 5% of however many total genes were tested to be false positives.\r\n\r\n"}}
{"actor":{"display_login":"oganm"}}