{"action":"created","issue":{"url":"https://api.github.com/repos/statOmics/zinbwaveZinger/issues/2","repository_url":"https://api.github.com/repos/statOmics/zinbwaveZinger","labels_url":"https://api.github.com/repos/statOmics/zinbwaveZinger/issues/2/labels{/name}","comments_url":"https://api.github.com/repos/statOmics/zinbwaveZinger/issues/2/comments","events_url":"https://api.github.com/repos/statOmics/zinbwaveZinger/issues/2/events","html_url":"https://github.com/statOmics/zinbwaveZinger/issues/2","id":332876695,"node_id":"MDU6SXNzdWUzMzI4NzY2OTU=","number":2,"title":"can't get zinbFit to finish","user":{"login":"friedue","id":4973546,"node_id":"MDQ6VXNlcjQ5NzM1NDY=","avatar_url":"https://avatars0.githubusercontent.com/u/4973546?v=4","gravatar_id":"","url":"https://api.github.com/users/friedue","html_url":"https://github.com/friedue","followers_url":"https://api.github.com/users/friedue/followers","following_url":"https://api.github.com/users/friedue/following{/other_user}","gists_url":"https://api.github.com/users/friedue/gists{/gist_id}","starred_url":"https://api.github.com/users/friedue/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/friedue/subscriptions","organizations_url":"https://api.github.com/users/friedue/orgs","repos_url":"https://api.github.com/users/friedue/repos","events_url":"https://api.github.com/users/friedue/events{/privacy}","received_events_url":"https://api.github.com/users/friedue/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":12,"created_at":"2018-06-15T18:40:09Z","updated_at":"2018-06-18T13:53:16Z","closed_at":null,"author_association":"NONE","body":"Hi,\r\n\r\nI've been trying to follow the strategy for DE using `zinbwave` as specified [here](https://github.com/statOmics/zinbwaveZinger/blob/master/realdata/usoskin/deAnalysis.Rmd) and I keep on running into the same error. Since this takes a rather long time to compute and I couldn't immediately spot the function that may issue the error, I was wondering whether you could point me to the culprit.\r\n\r\n```\r\nzinb <- zinbFit(core, X = design, commondispersion = TRUE, epsilon=1e12, verbose = TRUE, maxiter.optimize = 2)\r\nCreate model:\r\nok\r\nInitialize parameters:\r\n\r\nok\r\nOptimize parameters:\r\nIteration 1\r\npenalized log-likelihood = -149172106.416477\r\nAfter dispersion optimization = -149172106.416477\r\n^[[A^[[B^[[B    user   system  elapsed\r\n68311.71    68.54 66309.15\r\nAfter right optimization = -149172106.416477\r\nAfter orthogonalization = -149172106.416477\r\n     user    system   elapsed\r\n73520.612    63.835  7400.819\r\nAfter left optimization = -149172106.416477\r\nAfter orthogonalization = -149172106.416477\r\nIteration 2\r\npenalized log-likelihood = -128545935.423954\r\nAfter dispersion optimization = -149172106.416477\r\nError in updt[[as.integer(i)]] <- .error(msg) :\r\n  attempt to select more than one element in integerOneIndex\r\nIn addition: Warning message:\r\nIn value[[3L]](cond) : NAs introduced by coercion\r\n```\r\n\r\n`core` is a SummarizedExperiment object with the following specs\r\n\r\n```\r\n> dim(core)\r\n[1] 15347 18329\r\n\r\n> str(core)\r\nFormal class 'SummarizedExperiment' [package \"SummarizedExperiment\"] with 5 slots\r\n  ..@ colData        :Formal class 'DataFrame' [package \"S4Vectors\"] with 6 slots\r\n  .. .. ..@ rownames       : chr [1:18329] \"D1\" \"D2\" \"D3\" \"D4\" ...\r\n  .. .. ..@ nrows          : int 18329\r\n  .. .. ..@ listData       :List of 1\r\n  .. .. .. ..$ condition: Ord.factor w/ 3 levels \"W\"<\"H\"<\"D\": 3 3 3 3 3 3 3 3 3 3 ...\r\n  .. .. ..@ elementType    : chr \"ANY\"\r\n  .. .. ..@ elementMetadata: NULL\r\n  .. .. ..@ metadata       : list()\r\n  ..@ assays         :Reference class 'ShallowSimpleListAssays' [package \"SummarizedExperiment\"] with 1 field\r\n  .. ..$ data: NULL\r\n  .. ..and 14 methods.\r\n  ..@ NAMES          : chr [1:15347] \"ENSMUSG00000033845\" \"ENSMUSG00000025903\" \"ENSMUSG00000033793\" \"ENSMUSG00000025907\" ...\r\n  ..@ elementMetadata:Formal class 'DataFrame' [package \"S4Vectors\"] with 6 slots\r\n  .. .. ..@ rownames       : NULL\r\n  .. .. ..@ nrows          : int 15347\r\n  .. .. ..@ listData       : Named list()\r\n  .. .. ..@ elementType    : chr \"ANY\"\r\n  .. .. ..@ elementMetadata: NULL\r\n  .. .. ..@ metadata       : list()\r\n  ..@ metadata       : list()\r\n```"},"comment":{"url":"https://api.github.com/repos/statOmics/zinbwaveZinger/issues/comments/398061574","html_url":"https://github.com/statOmics/zinbwaveZinger/issues/2#issuecomment-398061574","issue_url":"https://api.github.com/repos/statOmics/zinbwaveZinger/issues/2","id":398061574,"node_id":"MDEyOklzc3VlQ29tbWVudDM5ODA2MTU3NA==","user":{"login":"drisso","id":8451432,"node_id":"MDQ6VXNlcjg0NTE0MzI=","avatar_url":"https://avatars0.githubusercontent.com/u/8451432?v=4","gravatar_id":"","url":"https://api.github.com/users/drisso","html_url":"https://github.com/drisso","followers_url":"https://api.github.com/users/drisso/followers","following_url":"https://api.github.com/users/drisso/following{/other_user}","gists_url":"https://api.github.com/users/drisso/gists{/gist_id}","starred_url":"https://api.github.com/users/drisso/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/drisso/subscriptions","organizations_url":"https://api.github.com/users/drisso/orgs","repos_url":"https://api.github.com/users/drisso/repos","events_url":"https://api.github.com/users/drisso/events{/privacy}","received_events_url":"https://api.github.com/users/drisso/received_events","type":"User","site_admin":false},"created_at":"2018-06-18T13:53:16Z","updated_at":"2018-06-18T13:53:16Z","author_association":"COLLABORATOR","body":"HI @jpvert \r\n\r\nthanks for spotting this! I hadn't noticed, mostly because I never use the `verbose` option and I think we don't have unit tests for this.\r\n\r\nI will have a look at what's going on (opening an issue in the `zinbwave` repo).\r\n\r\n"}}
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