{"action":"created","issue":{"url":"https://api.github.com/repos/biocore/scikit-bio/issues/1524","repository_url":"https://api.github.com/repos/biocore/scikit-bio","labels_url":"https://api.github.com/repos/biocore/scikit-bio/issues/1524/labels{/name}","comments_url":"https://api.github.com/repos/biocore/scikit-bio/issues/1524/comments","events_url":"https://api.github.com/repos/biocore/scikit-bio/issues/1524/events","html_url":"https://github.com/biocore/scikit-bio/issues/1524","id":243731399,"number":1524,"title":"skbio.stats.composition - ancom runtime warning: invalid value encountered in double_scalars","user":{"login":"handibles","id":26572263,"avatar_url":"https://avatars0.githubusercontent.com/u/26572263?v=4","gravatar_id":"","url":"https://api.github.com/users/handibles","html_url":"https://github.com/handibles","followers_url":"https://api.github.com/users/handibles/followers","following_url":"https://api.github.com/users/handibles/following{/other_user}","gists_url":"https://api.github.com/users/handibles/gists{/gist_id}","starred_url":"https://api.github.com/users/handibles/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/handibles/subscriptions","organizations_url":"https://api.github.com/users/handibles/orgs","repos_url":"https://api.github.com/users/handibles/repos","events_url":"https://api.github.com/users/handibles/events{/privacy}","received_events_url":"https://api.github.com/users/handibles/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2017-07-18T14:15:09Z","updated_at":"2017-07-18T15:53:54Z","closed_at":null,"body":"Firstly, apologies if this is not the place for more community-orientated support, but I couldn't see an alternative channel.\r\n\r\n   My OTU data has come through QIIME and phyloseq, exported to text and then into python.\r\n\r\n   I'm using multiplicative_replacement on an OTU table, then testing with defaults in ancom over two uneven-sized groups (10,4). When run, I receive a warning but am unsure if I should be concerned about it, as I still receive the expected output.\r\n\r\n   Multiplicative replacement should remove 0 values from my OTU table - is this an issue with tiny pseudocounts reverting to zero? Or something more fundamental? \r\n\r\n```\r\n# imported pandas, skbio, scipy\r\notu_rep = mult_rep(otu)\r\nindex = otu.index.values\r\ncolumns = otu.columns.values\r\notu_rep = pd.DataFrame(otu_rep,index=index,columns=columns)\r\ngroupA=pd.Series(['1','1','1','1','1','1','1','1','1','1','2','2','2','2'],index=[index])\r\nresultsA = ancom(otu_rep,groupA)\r\n\r\n**/home/cith/miniconda3/lib/python3.6/site-packages/scipy/stats/stats.py:2968: RuntimeWarning: invalid value encountered in double_scalars\r\n  f = msb / msw**\r\n```\r\n\r\nthanks for your time.\r\n"},"comment":{"url":"https://api.github.com/repos/biocore/scikit-bio/issues/comments/316109385","html_url":"https://github.com/biocore/scikit-bio/issues/1524#issuecomment-316109385","issue_url":"https://api.github.com/repos/biocore/scikit-bio/issues/1524","id":316109385,"user":{"login":"handibles","id":26572263,"avatar_url":"https://avatars0.githubusercontent.com/u/26572263?v=4","gravatar_id":"","url":"https://api.github.com/users/handibles","html_url":"https://github.com/handibles","followers_url":"https://api.github.com/users/handibles/followers","following_url":"https://api.github.com/users/handibles/following{/other_user}","gists_url":"https://api.github.com/users/handibles/gists{/gist_id}","starred_url":"https://api.github.com/users/handibles/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/handibles/subscriptions","organizations_url":"https://api.github.com/users/handibles/orgs","repos_url":"https://api.github.com/users/handibles/repos","events_url":"https://api.github.com/users/handibles/events{/privacy}","received_events_url":"https://api.github.com/users/handibles/received_events","type":"User","site_admin":false},"created_at":"2017-07-18T15:53:54Z","updated_at":"2017-07-18T15:53:54Z","body":"Thanks @mortonjt .  I should have mentioned also that I've tried it with two different datasets and receive the same error in either. Small subset OTU table supplied provides the error.\r\n\r\n \r\n[h_curtailed.txt](https://github.com/biocore/scikit-bio/files/1156462/h_curtailed.txt)\r\n"}}
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