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wguo-research / scCancer

A package for automated processing of single cell RNA-seq data in cancer
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Error in plotMarkerDistribution(sc): Failed as no clusters found! Clustering must be set via 'setClusters' to find marker genes. #20

Closed honghh2018 closed 4 years ago

honghh2018 commented 4 years ago

Hi @wguo, Thanks to develop the great tools for single cell cancer analysis. There some issue occured when runing the scCancer. The function runScStatistics had show error as running on the step 5 like below info.

  1. plotMarkerDistribution(sc)
    1. stop("Failed as no clusters found! Clustering must be set via 'setClusters' to find marker genes.") The error indicate that whether matrix should be run into seurat and find the cluster or not ? Meanwhile, i found your guide that post in the web https://github.com/wguo-research/scCancer/wiki/3.-Quick-start' had never exhibited the executed clustering before runing the runScStatistics function. Addtionanlly, the function runScStatistics workflow just import the data that ouput from 10x cellranger count like below picture and it should be clustering first or should some steps be execute first before runing function runScStatistics ?.

image

wguo-research commented 4 years ago

When did you install our package? You can reinstall the latest version and try it again. If the error continue, please contact me.