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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.

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Error in quantile.default(x, 1 - cap) : missing values and NaN's not allowed if 'na.rm' is FALSE

cubense opened this issue · comments

commented

Dear Dr livnatje:
Thank you for your wonderful software,
when I run the DIALOGUE.run,the error report:
...
[1] "#************DIALOGUE Step II (multilevel modeling): Hepatocyte vs. Stellate ************#"
[1] "1 MCPs identified for these cell types."
boundary (singular) fit: see ?isSingular
boundary (singular) fit: see ?isSingular
[1] "#Finalizing the scores#"
[1] "./DIALOGUE2_kmhs.rds"
NULL
NULL
NULL
Error in quantile.default(x, 1 - cap) :
missing values and NaN's not allowed if 'na.rm' is FALSE

what shall i do can fix it,thank you !

commented

Hi @cubense! I am not sure why you are getting this error.
Would help if you could provide the input (or a subset of it) so I could help you troubleshoot this.

Thanks!

commented

Thanks for your reply, I'm sure it's a problem with using nmf as X. It reported this error when I constructed the list using tumor cells constructed with the score matrix from nmf along with other celltypes constructed using principal components. Due to the amount of data, I uploaded the x matrix
x.csv

commented

Thanks for sharing the data @cubense. I will look into that and get back to you asap. DIALOGUE should be able to run with NMF. Were you able to run it when providing the PCs for all cell types?