{"action":"created","issue":{"url":"https://api.github.com/repos/LiNk-NY/RTCGAToolbox/issues/4","labels_url":"https://api.github.com/repos/LiNk-NY/RTCGAToolbox/issues/4/labels{/name}","comments_url":"https://api.github.com/repos/LiNk-NY/RTCGAToolbox/issues/4/comments","events_url":"https://api.github.com/repos/LiNk-NY/RTCGAToolbox/issues/4/events","html_url":"https://github.com/LiNk-NY/RTCGAToolbox/issues/4","id":97199970,"number":4,"title":"Extract function","user":{"login":"aedin","id":714323,"avatar_url":"https://avatars.githubusercontent.com/u/714323?v=3","gravatar_id":"","url":"https://api.github.com/users/aedin","html_url":"https://github.com/aedin","followers_url":"https://api.github.com/users/aedin/followers","following_url":"https://api.github.com/users/aedin/following{/other_user}","gists_url":"https://api.github.com/users/aedin/gists{/gist_id}","starred_url":"https://api.github.com/users/aedin/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/aedin/subscriptions","organizations_url":"https://api.github.com/users/aedin/orgs","repos_url":"https://api.github.com/users/aedin/repos","events_url":"https://api.github.com/users/aedin/events{/privacy}","received_events_url":"https://api.github.com/users/aedin/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-07-25T06:14:13Z","updated_at":"2015-08-06T23:57:25Z","closed_at":null,"body":"Hi \r\nWhen there is more than one object, extract should list the options and 1) say which object it is selecting and 2) provide the option to select a different one. (or all).  in the resulting expression set, the annotation slot should specify the filename\r\n\r\nfor example, in the  tcga ovarian, there are 4 microarray platforms, extract chooses one and ignores the rest\r\n\r\n> sapply(ov@mRNAArray, function(x) dim(x@DataMatrix))\r\n      [,1]  [,2]  [,3]  [,4]\r\n[1,] 17814 17814 12042 18632\r\n[2,]    36   561   593   594\r\n\r\n> sapply(ov@mRNAArray, function(x) x@Filename)\r\n[1] \"gdac.broadinstitute.org_OV.Merge_transcriptome__agilentg4502a_07_2__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.Level_3.2015040200.0.0.tar.gz\"\r\n[2] \"gdac.broadinstitute.org_OV.Merge_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.Level_3.2015040200.0.0.tar.gz\"\r\n[3] \"gdac.broadinstitute.org_OV.Merge_transcriptome__ht_hg_u133a__broad_mit_edu__Level_3__gene_rma__data.Level_3.2015040200.0.0.tar.gz\"                            \r\n[4] \"gdac.broadinstitute.org_OV.Merge_exon__huex_1_0_st_v2__lbl_gov__Level_3__quantile_normalization_gene__data.Level_3.2015040200.0.0.tar.gz\"  \r\n\r\n\r\naedin"},"comment":{"url":"https://api.github.com/repos/LiNk-NY/RTCGAToolbox/issues/comments/128541948","html_url":"https://github.com/LiNk-NY/RTCGAToolbox/issues/4#issuecomment-128541948","issue_url":"https://api.github.com/repos/LiNk-NY/RTCGAToolbox/issues/4","id":128541948,"user":{"login":"LiNk-NY","id":4392950,"avatar_url":"https://avatars.githubusercontent.com/u/4392950?v=3","gravatar_id":"","url":"https://api.github.com/users/LiNk-NY","html_url":"https://github.com/LiNk-NY","followers_url":"https://api.github.com/users/LiNk-NY/followers","following_url":"https://api.github.com/users/LiNk-NY/following{/other_user}","gists_url":"https://api.github.com/users/LiNk-NY/gists{/gist_id}","starred_url":"https://api.github.com/users/LiNk-NY/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/LiNk-NY/subscriptions","organizations_url":"https://api.github.com/users/LiNk-NY/orgs","repos_url":"https://api.github.com/users/LiNk-NY/repos","events_url":"https://api.github.com/users/LiNk-NY/events{/privacy}","received_events_url":"https://api.github.com/users/LiNk-NY/received_events","type":"User","site_admin":false},"created_at":"2015-08-06T23:57:25Z","updated_at":"2015-08-06T23:57:25Z","body":"I added a user prompt for selecting one file. "}}