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Denoising scRNA-seq using DCA can not work

Open peibana opened this issue 1 year ago • 0 comments

hello! when I'm running what you provided[tutorial.ipynb](https://github.com/theislab/dca/blob/master/tutorial.ipynb),my RStudio prompts me with the following error:

> source("D:/RHome/smi/dca_tutorial.R")
Getting parameters...
Creating simulation object...
Simulating library sizes...
Simulating gene means...
Simulating group DE...
Simulating cell means...
Simulating BCV...
Simulating counts...
Simulating dropout (if needed)...
Sparsifying assays...
Automatically converting to sparse matrices, threshold = 0.95
Skipping 'BatchCellMeans': estimated sparse size 1.5 * dense matrix
Skipping 'BaseCellMeans': estimated sparse size 1.5 * dense matrix
Skipping 'BCV': estimated sparse size 1.5 * dense matrix
Skipping 'CellMeans': estimated sparse size 1.5 * dense matrix
Skipping 'TrueCounts': estimated sparse size 2.86 * dense matrix
Skipping 'DropProb': estimated sparse size 1.5 * dense matrix
Converting 'Dropout' to sparse matrix: estimated sparse size 0.56 * dense matrix
Skipping 'counts': estimated sparse size 2.17 * dense matrix
Done!
Error in mde(x) : cannot coerce type 'S4' to vector of type 'integer'

But when I replace 'simulate <- function(nGroups=2, nGenes=200, batchCells=2000, dropout=3)' with 'simulate <- function(nGroups=2, nGenes=1000, batchCells=2000, dropout=4)', the code works fine. The input taken is the input provided in GitHub. I don't understand where the problem is, look forward to your reply.

The version information of the package is as follows: splatter 1.22.1 R 4.2.2

peibana avatar Mar 05 '23 12:03 peibana