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cole-trapnell-lab
Error in orderCells: long vectors not supported yet
Hi guys,
I'm using monocle on a big dataset (>50k cells). I'm getting this error calling the orderCells function:
Error in graph.adjacency.dense(adjmatrix, mode = mode, weighted = weighted, : long vectors not supported yet: ../../src/include/Rinlinedfuns.h:138 Calls: orderCells ... project2MST -> graph.adjacency -> graph.adjacency.dense -> .Call
I'm sure I'm using a sparse Matrix. I suppose this could be a problem in igraph or even in R core functions. Can anybody help me fix it? Thx, Marco.
Hi @marcovito, we are overhauling the reduceDimension and orderCells functions now. It will support analyzing millions of cells. This issue will be fixed soon!
Hi, I ran into the same problem... I would like to know whether this issue has been fixed. Thanks! Lei
Hi, I ran into the same problem too. Is there any good solutions to the problem? Thx, Shine.
Yeah — just started! Looking forward to the official release...
On Jan 8, 2019, at 23:44, Xiaojie Qiu <[email protected]mailto:[email protected]> wrote:
Hey, are you guys using monocle3-alpha?
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we will hopefully release it in near future. Monocle 3alpha should easily handle 50 k cells. please let me if there are any future issues
Ehm, how about 1.5 million? :)
On Jan 8, 2019, at 23:49, Xiaojie Qiu <[email protected]mailto:[email protected]> wrote:
we will hopefully release it in near future. Monocle 3alpha should easily handle 50 k cells. please let me if there are any future issues
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it depends. If your data is sparse enough and all 1.5 million cell data can be put into a single sparse matrix, it should work just fine. Unfortunately R is limited to store 2^31-1 bit data for a single sparse matrix (or vector), so anything larger than that seems not feasible to keep in memory. If your data is not able to store in a sparse matrix, consider taking only the top 1000 variable genes or so and then do the downstream analysis.
There are plans to rewrite most monocle functions to support hdf5 so that we only connect a hdf5 file on disk and manipulate chunks of data each time in memory.
Hi! Has anyone solved this problem? `> cds <- setOrderingFilter(cds_obj, ordergene)
dim(cds) Features Samples 2000 53794 cds <- reduceDimension(cds, max_components = 2,method = 'DDRTree') Warning messages: 1: In eval(call, parent.frame()) : NaNs produced 2: Quick-TRANSfer stage steps exceeded maximum (= 2689700) cds <- orderCells(cds) Error in graph.adjacency.dense(adjmatrix, mode = mode, weighted = weighted, : long vectors not supported yet: ../../src/include/Rinlinedfuns.h:537 In addition: There were 50 or more warnings (use warnings() to see the first 50)`
Hi guys,
I'm using monocle on a big dataset (>50k cells). I'm getting this error calling the orderCells function:
Error in graph.adjacency.dense(adjmatrix, mode = mode, weighted = weighted, : long vectors not supported yet: ../../src/include/Rinlinedfuns.h:138 Calls: orderCells ... project2MST -> graph.adjacency -> graph.adjacency.dense -> .Call
I'm sure I'm using a sparse Matrix. I suppose this could be a problem in igraph or even in R core functions. Can anybody help me fix it? Thx, Marco.
The error occured might be the larger number cells. When I randomly sampled 5000 cells，it works.
Hi guys, I'm using monocle on a big dataset (>50k cells). I'm getting this error calling the orderCells function: Error in graph.adjacency.dense(adjmatrix, mode = mode, weighted = weighted, : long vectors not supported yet: ../../src/include/Rinlinedfuns.h:138 Calls: orderCells ... project2MST -> graph.adjacency -> graph.adjacency.dense -> .Call I'm sure I'm using a sparse Matrix. I suppose this could be a problem in igraph or even in R core functions. Can anybody help me fix it? Thx, Marco.
The error occured might be the larger number cells. When I randomly sampled 5000 cells，it works.
@ZivTQ Dear ZivTQ,
I hope this message finds you well. I've encountered the same error, and I was wondering if you could provide more information about the code related to "randomly sampled 5000 cells" that you mentioned. Could you please share the specific code and let me know which step it should be added to?
Thx, Lin
Hi guys, I'm using monocle on a big dataset (>50k cells). I'm getting this error calling the orderCells function: Error in graph.adjacency.dense(adjmatrix, mode = mode, weighted = weighted, : long vectors not supported yet: ../../src/include/Rinlinedfuns.h:138 Calls: orderCells ... project2MST -> graph.adjacency -> graph.adjacency.dense -> .Call I'm sure I'm using a sparse Matrix. I suppose this could be a problem in igraph or even in R core functions. Can anybody help me fix it? Thx, Marco.
The error occured might be the larger number cells. When I randomly sampled 5000 cells，it works.
@ZivTQ Dear ZivTQ,
I hope this message finds you well. I've encountered the same error, and I was wondering if you could provide more information about the code related to "randomly sampled 5000 cells" that you mentioned. Could you please share the specific code and let me know which step it should be added to?
Thx, Lin
I think maybe use sce<-subset(sce, downsample = 1000),this will downsample by ident and get smaller data
I met the same problem and the data dim is Features= 26465 Samples=50634 I wonder in R how many cells monocle can handle at most