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welch-lab / cytosignal

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cs <- findNN(cs) is generating error #6

Closed anne04 closed 4 months ago

anne04 commented 4 months ago

findNN(cs) is generating error when I am executing the tutorial from this site: https://htmlpreview.github.io/?https://github.com/welch-lab/cytosignal/blob/master/doc/cytosignal.html

The screenshot is provided below:

Screenshot from 2024-04-23 16-18-14

skpalan commented 4 months ago

Thanks for your interest. However, I was not able to reproduce the error with our demo data. Which platform are you using?

anne04 commented 4 months ago

I am using CentOS Linux.

mvfki commented 4 months ago

@anne04 Did you run the Preprocessing steps? The scale factor is internally pre-computed during removeLowQuality() and I can see the same error message if I skip that code chunk.

anne04 commented 4 months ago

Thank you! You are right, I was skipping the preprocessing. It was a mistake on my end. Sorry to bother you. After doing that everything is working.

mvfki commented 4 months ago

All good! Although those are steps not supposed to be skipped, we will try to optimize the workflow a bit to see if such errors can be eliminated.