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

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 #18

Open cubense opened 2 years ago

cubense commented 2 years ago

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 !

livnatje commented 2 years ago

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!

cubense commented 2 years ago

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

livnatje commented 2 years ago

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?