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seen this several times now: When manually picking peaks in the EIC window, I get one set of peaks grouped together. But doing DB search, I get a different set of peaks grouped. I would like to get a better handle on what causes this difference, what the relevant parameters are, and whether it's possible to get consistent behavior, or whether that's undesirable for some reason.\r\n\r\nI think this requires several of us to look at the code together and talk about what the differences are and why it may have been written the way it was.\r\n\r\nPS. This is anecdotal, but in general I feel like I get \"better\" grouping when doing manual picking in the EIC window."},"comment":{"url":"https://api.github.com/repos/ElucidataInc/ElMaven/issues/comments/432724861","html_url":"https://github.com/ElucidataInc/ElMaven/issues/103#issuecomment-432724861","issue_url":"https://api.github.com/repos/ElucidataInc/ElMaven/issues/103","id":432724861,"node_id":"MDEyOklzc3VlQ29tbWVudDQzMjcyNDg2MQ==","user":{"login":"shubhra-agrawal","id":28925846,"node_id":"MDQ6VXNlcjI4OTI1ODQ2","avatar_url":"https://avatars3.githubusercontent.com/u/28925846?v=4","gravatar_id":"","url":"https://api.github.com/users/shubhra-agrawal","html_url":"https://github.com/shubhra-agrawal","followers_url":"https://api.github.com/users/shubhra-agrawal/followers","following_url":"https://api.github.com/users/shubhra-agrawal/following{/other_user}","gists_url":"https://api.github.com/users/shubhra-agrawal/gists{/gist_id}","starred_url":"https://api.github.com/users/shubhra-agrawal/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/shubhra-agrawal/subscriptions","organizations_url":"https://api.github.com/users/shubhra-agrawal/orgs","repos_url":"https://api.github.com/users/shubhra-agrawal/repos","events_url":"https://api.github.com/users/shubhra-agrawal/events{/privacy}","received_events_url":"https://api.github.com/users/shubhra-agrawal/received_events","type":"User","site_admin":false},"created_at":"2018-10-24T16:16:04Z","updated_at":"2018-10-24T16:16:04Z","author_association":"COLLABORATOR","body":"> 1. The function that selects which peak is highlighted in the EIC widget is a ridiculously simple heuristic (`EICLogic::selectGroupNearRt`). It finds any groups within 2min of expectedRt and takes the one with the highest intensity.  Was this always like this? (Edit: just checked 776, it was the same, as expected). For some reason I thought it did something smarter. In any case, it's clear to change this to using the groupRank formula (with the weights determined by the user as in #90\r\n\r\nResolved\r\n\r\n> 2. I can't figure out any reason why grouping would be different between the EIC window and the automated peak detection. It looks like they both call `EIC::groupPeaks` and the parameters are taken from `settings`. Let me know if you have any guesses as to why they might produce different behaviors, and I will keep thinking about this also\r\n\r\nResolved as part of #265\r\n\r\n>  I would expect that unchecking the \"consider retention time\" box is equivalent to setting the \"dRT weight\" to zero.\r\n\r\nFiled as #422. It seems to be working on latest develop\r\n\r\nThe only unresolved conversation in this thread is around tweaking the rank formula to cover certain cases:\r\n\r\n> 1. change (deltaRt)^2C to ((deltaRt^2)+epsilon)^C. Some fraction (0.05?) of the peak width would be a good value for epsilon, that way if RT units change from minutes to seconds or something like that, we don't have to worry about our hard-coded value.\r\n> 2. let the sliders go up at least 10 or maybe 20 instead of 5 (if we make them log scale, even better, but not a big deal)\r\n> 3. I think that changing (log(intensity)+1)^B to something like (intensity+1)^0.1B would be a good idea. But since this would make the old behavior unrecoverable, we don't have to do it (I think having two different grouprank formulas is option overload)\r\n\r\nLet's move this conversation to #90 and close this thread? @chubukov "}}
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