{"action":"closed","issue":{"url":"https://api.github.com/repos/joey711/phyloseq/issues/447","labels_url":"https://api.github.com/repos/joey711/phyloseq/issues/447/labels{/name}","comments_url":"https://api.github.com/repos/joey711/phyloseq/issues/447/comments","events_url":"https://api.github.com/repos/joey711/phyloseq/issues/447/events","html_url":"https://github.com/joey711/phyloseq/issues/447","id":62538414,"number":447,"title":"How is the library size information incorporated into the estimate_richness function?","user":{"login":"sfujio","id":11312746,"avatar_url":"https://avatars.githubusercontent.com/u/11312746?v=3","gravatar_id":"","url":"https://api.github.com/users/sfujio","html_url":"https://github.com/sfujio","followers_url":"https://api.github.com/users/sfujio/followers","following_url":"https://api.github.com/users/sfujio/following{/other_user}","gists_url":"https://api.github.com/users/sfujio/gists{/gist_id}","starred_url":"https://api.github.com/users/sfujio/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/sfujio/subscriptions","organizations_url":"https://api.github.com/users/sfujio/orgs","repos_url":"https://api.github.com/users/sfujio/repos","events_url":"https://api.github.com/users/sfujio/events{/privacy}","received_events_url":"https://api.github.com/users/sfujio/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":1,"created_at":"2015-03-17T23:00:42Z","updated_at":"2015-03-18T19:54:41Z","closed_at":"2015-03-18T19:54:41Z","body":"Hi Joey,\r\nI have a follow up question from the closed Issue#287 How does estimate_richness deal with uneven sequencing depth? \r\n\r\nI have used plot_richness and estimate_richness with boxplot function to generate plots, and they have very large variance. I have seen that in many tutorials and in the #287 Issue, it is said not to trim or standardize the library size but also have come across with papers such as DOI: 10.1111/j.1462-2920.2011.02550.x and DOI: 10.1002/ece3.508 were it´s discussed that different library size would affect to the estimation of richness and diversity and that the sample´s library size should be standardize. Could you specify how is the library size information incorporated into the estimation? so I can justify why I used the raw data when I present my results.\r\n\r\nThank you\r\n\r\nPS: I have seen the word normalize used, after using the DESeq transformation of the data, but strictly speaking it should be standardize, because normalizing is transforming the data so it has a normal distribution, which I would think is not what happens when that command is used.. or is that what happens?"}}