{"action":"created","issue":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1404","repository_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen","labels_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1404/labels{/name}","comments_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1404/comments","events_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1404/events","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1404","id":156902042,"number":1404,"title":"Clustering in small rna report","user":{"login":"hmkim","id":4966343,"avatar_url":"https://avatars.githubusercontent.com/u/4966343?v=3","gravatar_id":"","url":"https://api.github.com/users/hmkim","html_url":"https://github.com/hmkim","followers_url":"https://api.github.com/users/hmkim/followers","following_url":"https://api.github.com/users/hmkim/following{/other_user}","gists_url":"https://api.github.com/users/hmkim/gists{/gist_id}","starred_url":"https://api.github.com/users/hmkim/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hmkim/subscriptions","organizations_url":"https://api.github.com/users/hmkim/orgs","repos_url":"https://api.github.com/users/hmkim/repos","events_url":"https://api.github.com/users/hmkim/events{/privacy}","received_events_url":"https://api.github.com/users/hmkim/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"milestone":null,"comments":4,"created_at":"2016-05-26T04:42:17Z","updated_at":"2016-05-27T03:55:58Z","closed_at":"2016-05-27T03:55:58Z","body":"Below, this is code in small rnaseq workflow.\r\n\r\n### Clustering\r\n```{r mirna-clustering, eval=ismirbase}\r\ncounts = counts(obj)\r\ndds = DESeqDataSetFromMatrix(counts[rowSums(counts>0)>3,], colData=design, design=~1)\r\nvst = rlog(dds)\r\n\r\npheatmap(assay(vst), annotation_col = design, show_rownames = F, \r\n         clustering_distance_cols = \"correlation\",\r\n         clustering_method = \"ward.D\")\r\n```\r\n\r\nWhen I running the report script with my data, I got the error in R.\r\n\r\n> dds = DESeqDataSetFromMatrix(counts[rowSums(counts>0)>3,], colData=design, design=~1)\r\nconverting counts to integer mode\r\n> vst = rlog(dds)\r\nError in estimateSizeFactorsForMatrix(counts(object), locfunc = locfunc,  : \r\n  every gene contains at least one zero, cannot compute log geometric means\r\n\r\n![2016-05-26 13 41 54](https://cloud.githubusercontent.com/assets/4966343/15563860/a787330a-2347-11e6-9a5b-986862ae8875.png)\r\n"},"comment":{"url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/comments/222054506","html_url":"https://github.com/chapmanb/bcbio-nextgen/issues/1404#issuecomment-222054506","issue_url":"https://api.github.com/repos/chapmanb/bcbio-nextgen/issues/1404","id":222054506,"user":{"login":"hmkim","id":4966343,"avatar_url":"https://avatars.githubusercontent.com/u/4966343?v=3","gravatar_id":"","url":"https://api.github.com/users/hmkim","html_url":"https://github.com/hmkim","followers_url":"https://api.github.com/users/hmkim/followers","following_url":"https://api.github.com/users/hmkim/following{/other_user}","gists_url":"https://api.github.com/users/hmkim/gists{/gist_id}","starred_url":"https://api.github.com/users/hmkim/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/hmkim/subscriptions","organizations_url":"https://api.github.com/users/hmkim/orgs","repos_url":"https://api.github.com/users/hmkim/repos","events_url":"https://api.github.com/users/hmkim/events{/privacy}","received_events_url":"https://api.github.com/users/hmkim/received_events","type":"User","site_admin":false},"created_at":"2016-05-27T03:55:58Z","updated_at":"2016-05-27T03:55:58Z","body":"@lpantano Thanks for your comment. I'll try to analyze with edgeR.\r\n@roryk Thanks for your reply.  I'll try it.\r\n"}}
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