{"action":"created","issue":{"url":"https://api.github.com/repos/MarioniLab/scran/issues/10","repository_url":"https://api.github.com/repos/MarioniLab/scran","labels_url":"https://api.github.com/repos/MarioniLab/scran/issues/10/labels{/name}","comments_url":"https://api.github.com/repos/MarioniLab/scran/issues/10/comments","events_url":"https://api.github.com/repos/MarioniLab/scran/issues/10/events","html_url":"https://github.com/MarioniLab/scran/issues/10","id":324520586,"number":10,"title":"mnnCorrect output generates error when calculating TSNE","user":{"login":"MwrulesC","id":5239985,"avatar_url":"https://avatars0.githubusercontent.com/u/5239985?v=4","gravatar_id":"","url":"https://api.github.com/users/MwrulesC","html_url":"https://github.com/MwrulesC","followers_url":"https://api.github.com/users/MwrulesC/followers","following_url":"https://api.github.com/users/MwrulesC/following{/other_user}","gists_url":"https://api.github.com/users/MwrulesC/gists{/gist_id}","starred_url":"https://api.github.com/users/MwrulesC/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/MwrulesC/subscriptions","organizations_url":"https://api.github.com/users/MwrulesC/orgs","repos_url":"https://api.github.com/users/MwrulesC/repos","events_url":"https://api.github.com/users/MwrulesC/events{/privacy}","received_events_url":"https://api.github.com/users/MwrulesC/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":6,"created_at":"2018-05-18T19:07:36Z","updated_at":"2018-05-21T19:12:41Z","closed_at":null,"author_association":"NONE","body":"Hi, I don't have much experience with scran, but I've recently been testing the use of mnnCorrect on some of the samples I have. Everything seems to work and I can generate figures up until I try to run TSNE calculations on the generated output. At that point I get the error message:\r\nError in svd(x, nu = 0, nv = k) : a dimension is zero\r\n\r\nAfter some digging around, I haven't quite figured out how to solve this error message in this particular instance. I was just wondering if you've had experience with something like this before, and if I should be doing some extra filtering or normalization pre/post analysis to avoid this.\r\n\r\nThe general overview of the code I use is the following:\r\n\r\nrawData <- Read10X(filepath1)\r\nfixed <- SingleCellExperiment(assays = list(counts=as.matrix(rawData)), colData = list(Sample = rep('Fixed',dim(rawData)[2])))\r\nfixed <- computeSumFactors(fixed)\r\nfixed <- normalize(fixed)\r\n\r\nrawData <- Read10X(filepath2)\r\nmixed  <- SingleCellExperiment(assays = list(counts=as.matrix(rawData)), colData = list(Sample = rep('Mixed',dim(rawData)[2])))\r\nmixed <- computeSumFactors(mixed)\r\nmixed <- normalize(mixed)\r\n\r\nout <- mnnCorrect(fixed@assays$data$logcounts, mixed@assays$data$logcounts)\r\n\r\nmixed@assays$data$mnnCounts <- out$corrected[[2]]\r\nfixed@assays$data$mnnCounts <- out$corrected[[1]]\r\ncombined <- cbind(fixed, mixed)\r\ncombined <- runPCA(combined, exprs_values = \"mnnCounts\")\r\nplotReducedDim(combined, use_dimred = \"PCA\", \r\n               colour_by = \"Sample\", shape_by = \"Sample\")\r\n\r\ncombined <- runTSNE(combined, exprs_values = \"logcounts\")\r\nplotTSNE(combined, colour_by = \"Sample\", shape_by = \"Sample\")\r\n\r\nThanks"},"comment":{"url":"https://api.github.com/repos/MarioniLab/scran/issues/comments/390753254","html_url":"https://github.com/MarioniLab/scran/issues/10#issuecomment-390753254","issue_url":"https://api.github.com/repos/MarioniLab/scran/issues/10","id":390753254,"user":{"login":"LTLA","id":8166669,"avatar_url":"https://avatars3.githubusercontent.com/u/8166669?v=4","gravatar_id":"","url":"https://api.github.com/users/LTLA","html_url":"https://github.com/LTLA","followers_url":"https://api.github.com/users/LTLA/followers","following_url":"https://api.github.com/users/LTLA/following{/other_user}","gists_url":"https://api.github.com/users/LTLA/gists{/gist_id}","starred_url":"https://api.github.com/users/LTLA/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/LTLA/subscriptions","organizations_url":"https://api.github.com/users/LTLA/orgs","repos_url":"https://api.github.com/users/LTLA/repos","events_url":"https://api.github.com/users/LTLA/events{/privacy}","received_events_url":"https://api.github.com/users/LTLA/received_events","type":"User","site_admin":false},"created_at":"2018-05-21T19:12:41Z","updated_at":"2018-05-21T19:12:41Z","author_association":"MEMBER","body":"The former; the order in which you pass batches to the `...` argument."}}
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