{"comment":{"url":"https://api.github.com/repos/transmart/Rmodules/comments/9201723","html_url":"https://github.com/transmart/Rmodules/commit/ae2419f16f1650f30f86d0c6616416747f19a207#commitcomment-9201723","id":9201723,"user":{"login":"weiguUL","id":9827960,"avatar_url":"https://avatars.githubusercontent.com/u/9827960?v=3","gravatar_id":"","url":"https://api.github.com/users/weiguUL","html_url":"https://github.com/weiguUL","followers_url":"https://api.github.com/users/weiguUL/followers","following_url":"https://api.github.com/users/weiguUL/following{/other_user}","gists_url":"https://api.github.com/users/weiguUL/gists{/gist_id}","starred_url":"https://api.github.com/users/weiguUL/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/weiguUL/subscriptions","organizations_url":"https://api.github.com/users/weiguUL/orgs","repos_url":"https://api.github.com/users/weiguUL/repos","events_url":"https://api.github.com/users/weiguUL/events{/privacy}","received_events_url":"https://api.github.com/users/weiguUL/received_events","type":"User","site_admin":false},"position":null,"line":null,"path":"","commit_id":"ae2419f16f1650f30f86d0c6616416747f19a207","created_at":"2015-01-08T13:38:13Z","updated_at":"2015-01-08T13:38:13Z","body":"Hi timdo,\r\n\r\nZ-score is not a requirement per se for hierarchical clustering (called here heatmap). One can perform z-score scaling for the heatmap data but it is not required to perform a “correct” hierarchical clutering. It depends on how the input data is. The previous version that uses pre-computed z-score is to our understanding quite wired, given the way the pre-computed z-scores are generated, this means they have been calculated on the complete study data available even though a user might only select a small subset of the samples available for defining the two cohorts. Such approach is problematic as z-score is pre-computed on a different data set then the one displayed using heat map.\r\n\r\nOne thing one may consider to add is to scale the input (e.g. by re-compute z-score calculation row-wise). For this there is a new commit available on Github.\r\n\r\nhttps://github.com/transmart/Rmodules/commit/ec4e733bfccd52a0c1a2221c03b0437b59916358 \r\n\r\nAnother thing is whether one want to truncate extreme values like those in the pre-computed z-score as it was in the previous MarkerSelection, this means one just truncates values where the z-score is above/below a certain threshold."}}