{"action":"closed","issue":{"url":"https://api.github.com/repos/MarioniLab/cydar/issues/1","repository_url":"https://api.github.com/repos/MarioniLab/cydar","labels_url":"https://api.github.com/repos/MarioniLab/cydar/issues/1/labels{/name}","comments_url":"https://api.github.com/repos/MarioniLab/cydar/issues/1/comments","events_url":"https://api.github.com/repos/MarioniLab/cydar/issues/1/events","html_url":"https://github.com/MarioniLab/cydar/issues/1","id":188012808,"number":1,"title":"Signalling molecule shifts","user":{"login":"ACRichard","id":19389147,"avatar_url":"https://avatars.githubusercontent.com/u/19389147?v=3","gravatar_id":"","url":"https://api.github.com/users/ACRichard","html_url":"https://github.com/ACRichard","followers_url":"https://api.github.com/users/ACRichard/followers","following_url":"https://api.github.com/users/ACRichard/following{/other_user}","gists_url":"https://api.github.com/users/ACRichard/gists{/gist_id}","starred_url":"https://api.github.com/users/ACRichard/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/ACRichard/subscriptions","organizations_url":"https://api.github.com/users/ACRichard/orgs","repos_url":"https://api.github.com/users/ACRichard/repos","events_url":"https://api.github.com/users/ACRichard/events{/privacy}","received_events_url":"https://api.github.com/users/ACRichard/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2016-11-08T14:56:17Z","updated_at":"2016-12-03T11:29:11Z","closed_at":"2016-12-03T11:29:11Z","body":"For signalling molecules that exhibit strong shifts in expression between conditions, cydar is very good at picking up differential abundance.  However, particularly in very high-dimensional data, if all other marker intensities are equal for a subpopulation and one condition only increases intensity of a signalling marker slightly, the shift will not be detected as a differentially abundant hypersphere.  In this situation, it may be beneficial to have the option to leave the signalling marker out of the initial hypersphere assigment phase of analysis and then compare median intensity of the signalling marker between conditions within a hypersphere. Of course, this will only work if the intensity of the whole subpopulation within the hypershere shifts, because if only a small fraction of the cells in the hypershere shift in signalling marker intensity, the median will not change and the shift will remain undetected."}}
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