{"action":"created","issue":{"url":"https://api.github.com/repos/nanoporetech/kmer_models/issues/7","repository_url":"https://api.github.com/repos/nanoporetech/kmer_models","labels_url":"https://api.github.com/repos/nanoporetech/kmer_models/issues/7/labels{/name}","comments_url":"https://api.github.com/repos/nanoporetech/kmer_models/issues/7/comments","events_url":"https://api.github.com/repos/nanoporetech/kmer_models/issues/7/events","html_url":"https://github.com/nanoporetech/kmer_models/issues/7","id":356215343,"node_id":"MDU6SXNzdWUzNTYyMTUzNDM=","number":7,"title":"Normalisation / scaling","user":{"login":"a-slide","id":5701192,"node_id":"MDQ6VXNlcjU3MDExOTI=","avatar_url":"https://avatars2.githubusercontent.com/u/5701192?v=4","gravatar_id":"","url":"https://api.github.com/users/a-slide","html_url":"https://github.com/a-slide","followers_url":"https://api.github.com/users/a-slide/followers","following_url":"https://api.github.com/users/a-slide/following{/other_user}","gists_url":"https://api.github.com/users/a-slide/gists{/gist_id}","starred_url":"https://api.github.com/users/a-slide/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/a-slide/subscriptions","organizations_url":"https://api.github.com/users/a-slide/orgs","repos_url":"https://api.github.com/users/a-slide/repos","events_url":"https://api.github.com/users/a-slide/events{/privacy}","received_events_url":"https://api.github.com/users/a-slide/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":4,"created_at":"2018-09-01T16:32:04Z","updated_at":"2018-09-03T10:27:58Z","closed_at":null,"author_association":"NONE","body":"Hi,\r\nHow did you normalise your data to obtain the level_mean for each kmer ? I suspect that it is based on albacore normalisation, so my question might actually be how Albacore is scaling the raw data ?  \r\nIs there any simple way to normalise the raw signal from fast5 files to get values matching those in the kmer model files (ie. scale and shift parameter) ?\r\nThanks\r\nAdrien"},"comment":{"url":"https://api.github.com/repos/nanoporetech/kmer_models/issues/comments/418072744","html_url":"https://github.com/nanoporetech/kmer_models/issues/7#issuecomment-418072744","issue_url":"https://api.github.com/repos/nanoporetech/kmer_models/issues/7","id":418072744,"node_id":"MDEyOklzc3VlQ29tbWVudDQxODA3Mjc0NA==","user":{"login":"cjw85","id":3592009,"node_id":"MDQ6VXNlcjM1OTIwMDk=","avatar_url":"https://avatars1.githubusercontent.com/u/3592009?v=4","gravatar_id":"","url":"https://api.github.com/users/cjw85","html_url":"https://github.com/cjw85","followers_url":"https://api.github.com/users/cjw85/followers","following_url":"https://api.github.com/users/cjw85/following{/other_user}","gists_url":"https://api.github.com/users/cjw85/gists{/gist_id}","starred_url":"https://api.github.com/users/cjw85/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/cjw85/subscriptions","organizations_url":"https://api.github.com/users/cjw85/orgs","repos_url":"https://api.github.com/users/cjw85/repos","events_url":"https://api.github.com/users/cjw85/events{/privacy}","received_events_url":"https://api.github.com/users/cjw85/received_events","type":"User","site_admin":false},"created_at":"2018-09-03T10:27:58Z","updated_at":"2018-09-03T10:27:58Z","author_association":"CONTRIBUTOR","body":"Not in general, again the values given for level_mean are contigent on the data that was used in their training. Due to variation between pores etc. there's no reason to expect the values for other data to be similar: at least a non-zero shift is required (maybe a non-unit scale).\r\n\r\nThe above is only really true for the deprecate HMM callers; the situation is further complicated by the fact that the \"events\" output by the RNN callers are simply fixed length blocks of raw data points, not a piece-wise constant modelling of the data."}}
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