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optimizeLSI for scRNA-seq gives Error in if (n < 0L) max(length(x) + n, 0L) else min(n, length(x)) :

Open CSBioAzim opened this issue 5 years ago • 0 comments

Hi, I've tried to run scRNA_01_Clustering_UMAP_v1.R using default parameters, and the "scRNA-All-Hematopoiesis-MPAL-191120.rds" as input. When I do run the #Optimize LSI Features lsiObj <- optimizeLSI(assay(se), resolution = resolution, pcsUse = nPCs, varFeatures = nTop)

it gives error after LSI 1 finished Number of communities: 38 Elapsed time: 188 seconds Additional LSI 2... Error in if (n < 0L) max(length(x) + n, 0L) else min(n, length(x)) : missing value where TRUE/FALSE needed

Anyone has faced with this error?

CSBioAzim avatar Feb 02 '20 19:02 CSBioAzim