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constantAmateur / SoupX

R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
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autoEstCont() error #118

Closed Polligator closed 2 years ago

Polligator commented 2 years ago

hi there, I tried to use SoupX manually by first reading in the raw and filtered count matrixes, to create a soup channel, then get the cluster info from Seurat, basically what is described here: https://cellgeni.github.io/notebooks/html/new-10kPBMC-SoupX.html

an error occurred when executing the command: soup.channel <- autoEstCont(soup.channel)

"Error in quantile.default(soupProf$est, soupQuantile) : missing values and NaN's not allowed if 'na.rm' is FALSE"

I could not figure out why the est were all calculated as Nans, please help count matrix was generated from cellranger 6.1.3, not sure if the version matters.

Thanks

xzhouaw commented 1 year ago

I am facing the same problem with manually loaded matrix. Could I know how you solved it?

JS0715 commented 1 year ago

Getting the same error. How did you fix this?