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reactome / ReactomeGSA

R client for the REACTOME Analysis Service for comparative multi-omics gene set analysis
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Error at too many cells – Cholmod error 'problem too large' #21

Closed vertesy closed 3 years ago

vertesy commented 3 years ago

Following the tutorial – worked on the example, tryin on my own data, I get a matrix size related error:

>   gsva_result <- analyse_sc_clusters(combined.obj, verbose = TRUE)
Calculating average cluster expression...
Error in asMethod(object) : 
  Cholmod error 'problem too large' at file ../Core/cholmod_dense.c, line 102

> combined.obj
An object of class Seurat 
28439 features across 158666 samples within 2 assays 
Active assay: integrated (2000 features, 2000 variable features)
 1 other assay present: RNA
 3 dimensional reductions calculated: pca, umap, tsne

I will try subsetting the dataset to 50%, 25% etc.

–––––––––––––––––––––––––––––– I used to get such errors when I used colSum etc that not explicitly from the matrix package.

vertesy commented 3 years ago

Down sampling to 30% solves the issue, however you might want to enable it for larger datasets.

jgriss commented 3 years ago

Hi,

It's a memory issue that's actually triggered by Seurat. Unfortunately, the only solution is to run your analysis on a larger machine or reduce the data size.

Kind regards, Johannes

On 2 June 2021 18:16:12 CEST, Abel Vertesy @.***> wrote:

Down sampling to 30% solves the issue, however you might want to enable it for larger datasets.

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