search

livnatje / DIALOGUE

DIALOGUE is a dimensionality reduction method that uses cross-cell-type associations to identify multicellular programs (MCPs) and map the cell transcriptome as a function of its environment.
Other
106 stars 16 forks source link

Trouble finishing MCP analysis with Seurat input #28

Closed VNurm closed 1 year ago

VNurm commented 2 years ago

The analysis runs fine, but when finilizing the analysis I run into trouble:

"#****Finalizing the scores****#" [1] "Removing MCP2" [1] "Removing MCP3" [1] "Removing MCP4" [1] "Removing MCP5" [1] "Removing MCP1" [1] "Removing MCP2" [1] "Removing MCP3" [1] "Removing MCP4" [1] "Removing MCP5" Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent

I've tried with several different parameters and cell.type inputs, and always get the same error.

Hopefully you can help!

Thanks!

OnkarMulay commented 1 year ago

Hi, Were you able to solve the issue?

livnatje commented 1 year ago

@OnkarMulay and @VNurm, are you running DIALOGUE on a small dataset? This issue can be the result of not finding any statistically significant MCPs, which is often due to small samples size.

Were you able to run the test set with the latest package? We've made some changes so best to reinstall.

VNurm commented 1 year ago

Hi,

Yeah, it's a fairly small dataset, and I originally suspected that it could be the major cause here, but wasn't sure.

I'll be sure to try it again with an expanded dataset using the new package!

Thank you very much!