{"action":"created","issue":{"url":"https://api.github.com/repos/satijalab/seurat/issues/520","repository_url":"https://api.github.com/repos/satijalab/seurat","labels_url":"https://api.github.com/repos/satijalab/seurat/issues/520/labels{/name}","comments_url":"https://api.github.com/repos/satijalab/seurat/issues/520/comments","events_url":"https://api.github.com/repos/satijalab/seurat/issues/520/events","html_url":"https://github.com/satijalab/seurat/issues/520","id":329100995,"node_id":"MDU6SXNzdWUzMjkxMDA5OTU=","number":520,"title":"Error Converting to loom file","user":{"login":"AshoorH","id":783288,"node_id":"MDQ6VXNlcjc4MzI4OA==","avatar_url":"https://avatars0.githubusercontent.com/u/783288?v=4","gravatar_id":"","url":"https://api.github.com/users/AshoorH","html_url":"https://github.com/AshoorH","followers_url":"https://api.github.com/users/AshoorH/followers","following_url":"https://api.github.com/users/AshoorH/following{/other_user}","gists_url":"https://api.github.com/users/AshoorH/gists{/gist_id}","starred_url":"https://api.github.com/users/AshoorH/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/AshoorH/subscriptions","organizations_url":"https://api.github.com/users/AshoorH/orgs","repos_url":"https://api.github.com/users/AshoorH/repos","events_url":"https://api.github.com/users/AshoorH/events{/privacy}","received_events_url":"https://api.github.com/users/AshoorH/received_events","type":"User","site_admin":false},"labels":[{"id":213735090,"node_id":"MDU6TGFiZWwyMTM3MzUwOTA=","url":"https://api.github.com/repos/satijalab/seurat/labels/bug","name":"bug","color":"fc2929","default":true}],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-06-04T15:17:54Z","updated_at":"2018-06-26T16:29:05Z","closed_at":null,"author_association":"NONE","body":"Hi, \r\n\r\nI am trying to convert Seurat object to loom file, when I run the provided example I got the following error: \r\n\r\n```R\r\n> library(loomR)\r\nLoading required package: R6\r\nLoading required package: hdf5r\r\nLoading required package: iterators\r\nLoading required package: itertools\r\n> library(Seurat)\r\nLoading required package: ggplot2\r\nLoading required package: cowplot\r\n\r\nAttaching package: ‘cowplot’\r\n\r\nThe following object is masked from ‘package:ggplot2’:\r\n\r\n    ggsave\r\n\r\nLoading required package: Matrix\r\n> data('pbmc_small')\r\n> lfile = Convert(from = pbmc_small, to = 'loom', filename = 'small.loom')\r\nTransposing input data: loom file will show input columns (cells) as rows and input rows (genes) as columns \r\nThis is to maintain compatibility with other loom tools \r\nError in dataset_create_pl$set_chunk(chunk_dims) : \r\n  In RToH5_INTEGER can't convert type of object passed\r\n\r\n```\r\nMay you advise on this issue? \r\n\r\nThanks\r\nHaitham"},"comment":{"url":"https://api.github.com/repos/satijalab/seurat/issues/comments/400377529","html_url":"https://github.com/satijalab/seurat/issues/520#issuecomment-400377529","issue_url":"https://api.github.com/repos/satijalab/seurat/issues/520","id":400377529,"node_id":"MDEyOklzc3VlQ29tbWVudDQwMDM3NzUyOQ==","user":{"login":"araksm","id":14058544,"node_id":"MDQ6VXNlcjE0MDU4NTQ0","avatar_url":"https://avatars2.githubusercontent.com/u/14058544?v=4","gravatar_id":"","url":"https://api.github.com/users/araksm","html_url":"https://github.com/araksm","followers_url":"https://api.github.com/users/araksm/followers","following_url":"https://api.github.com/users/araksm/following{/other_user}","gists_url":"https://api.github.com/users/araksm/gists{/gist_id}","starred_url":"https://api.github.com/users/araksm/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/araksm/subscriptions","organizations_url":"https://api.github.com/users/araksm/orgs","repos_url":"https://api.github.com/users/araksm/repos","events_url":"https://api.github.com/users/araksm/events{/privacy}","received_events_url":"https://api.github.com/users/araksm/received_events","type":"User","site_admin":false},"created_at":"2018-06-26T16:29:05Z","updated_at":"2018-06-26T16:29:05Z","author_association":"NONE","body":"Hi,\r\n\r\nI'm trying to convert my Seurat version 1.4 object to loom format using loom R.\r\nSo I update my object by \r\n> updatedObject <- UpdateSeuratObject (seurat1.4object).\r\n\r\nThen I'm converting it to loom by\r\n> lfile = Convert(from = updatedObject, to = 'loom', filename = 'output.loom')\r\n\r\n>Transposing input data: loom file will show input columns (cells) as rows and input rows (genes) as columns \r\n>This is to maintain compatibility with other loom tools \r\n>  |==============================================| 100%\r\n>Error in new.loom$add.layer(layer = layers) : \r\n>  All layers must have 1811 rows for cells and 49568 columns for genes\r\n\r\nI guess it is caused since my updatedObject@raw.data and updatedObject@scale.data are of different dimensions (the number of rows (genes) is different). So I was wondering are raw.data and scale.data supposed to have the same size?  If not, how could I fix that? Should I simply remove additional rows from the updatedObject@raw.data?\r\n\r\nThank you,\r\nAraks"}}
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