{"action":"opened","issue":{"url":"https://api.github.com/repos/seandavi/GEOquery/issues/25","labels_url":"https://api.github.com/repos/seandavi/GEOquery/issues/25/labels{/name}","comments_url":"https://api.github.com/repos/seandavi/GEOquery/issues/25/comments","events_url":"https://api.github.com/repos/seandavi/GEOquery/issues/25/events","html_url":"https://github.com/seandavi/GEOquery/issues/25","id":121895371,"number":25,"title":"Parsing of differing characteristics in Series Matrices makes phenodata messy","user":{"login":"seandavi","id":92435,"avatar_url":"https://avatars.githubusercontent.com/u/92435?v=3","gravatar_id":"","url":"https://api.github.com/users/seandavi","html_url":"https://github.com/seandavi","followers_url":"https://api.github.com/users/seandavi/followers","following_url":"https://api.github.com/users/seandavi/following{/other_user}","gists_url":"https://api.github.com/users/seandavi/gists{/gist_id}","starred_url":"https://api.github.com/users/seandavi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/seandavi/subscriptions","organizations_url":"https://api.github.com/users/seandavi/orgs","repos_url":"https://api.github.com/users/seandavi/repos","events_url":"https://api.github.com/users/seandavi/events{/privacy}","received_events_url":"https://api.github.com/users/seandavi/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/seandavi/GEOquery/labels/enhancement","name":"enhancement","color":"84b6eb"}],"state":"open","locked":false,"assignee":{"login":"seandavi","id":92435,"avatar_url":"https://avatars.githubusercontent.com/u/92435?v=3","gravatar_id":"","url":"https://api.github.com/users/seandavi","html_url":"https://github.com/seandavi","followers_url":"https://api.github.com/users/seandavi/followers","following_url":"https://api.github.com/users/seandavi/following{/other_user}","gists_url":"https://api.github.com/users/seandavi/gists{/gist_id}","starred_url":"https://api.github.com/users/seandavi/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/seandavi/subscriptions","organizations_url":"https://api.github.com/users/seandavi/orgs","repos_url":"https://api.github.com/users/seandavi/repos","events_url":"https://api.github.com/users/seandavi/events{/privacy}","received_events_url":"https://api.github.com/users/seandavi/received_events","type":"User","site_admin":false},"milestone":null,"comments":0,"created_at":"2015-12-13T03:30:15Z","updated_at":"2015-12-13T03:30:15Z","closed_at":null,"body":"Good day,\r\n\r\nI found an issue in the way that getGEO parses the clinical data. Consider\r\n\r\novaCancer <- getGEO(\"GSE53963\")[[1]]\r\npData(ovaCancer)[1:6, 20:25]\r\n          characteristics_ch2.1 characteristics_ch2.2 characteristics_ch2.3 characteristics_ch2.4 characteristics_ch2.5 characteristics_ch2.6\r\nGSM1304246    morphology: Serous            stage_#: 2             Stage: II           substage: B               grade: 4    debulking: Optimal\r\nGSM1304247    morphology: Serous            stage_#: 3            Stage: III           substage: C               grade: 4   debulking: Optimal\r\nGSM1304248    morphology: Serous            stage_#: 4             Stage: IV              grade: 3 debulking: Sub-optimal  time_fu_months: 1.12\r\nGSM1304249    morphology: Serous            stage_#: 3            Stage: III           substage: C               grade: 3   debulking: Optimal\r\nGSM1304250    morphology: Serous            stage_#: 3            Stage: III           substage: C               grade: 4   debulking: Optimal\r\nGSM1304251    morphology: Serous            stage_#: 4             Stage: IV              grade: 3 debulking: Sub-optimal time_fu_months: 47.20\r\n\r\nBecause stage 4 samples have no substage data, the alignment of the data into columns after the stage column is one column too left. Is it possible to handle this case automatically ?\r\n\r\n--------------------------------------\r\nDario Strbenac\r\nPhD Student\r\nUniversity of Sydney\r\nCamperdown NSW 2050\r\nAustralia"}}