sc3_kmeans produces "Warning message: Quick-TRANSfer stage steps exceeded maximum (= 250000)"

hemberg-lab / SC3

A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments

http://bioconductor.org/packages/SC3

GNU General Public License v3.0

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sc3_kmeans produces "Warning message: Quick-TRANSfer stage steps exceeded maximum (= 250000)" #100

Closed MikeHala closed 3 years ago

MikeHala commented 3 years ago

Dear SC3 developers,

I am running SC3 (1.12.0) on HPC with a dataset with ~10k cells and ~ 17k genes.

Running the step sce <- sc3_kmeans(sce, ks = 10:25), after reaching 100% on the progress bar, it produces a bunch of Warning messages: 1: Quick-TRANSfer stage steps exceeded maximum (= 250000) 2: Quick-TRANSfer stage steps exceeded maximum (= 250000) ...

Is this just a warning that can be safely ignored or some intervention is needed?

Best, Mike

wikiselev commented 3 years ago

Hi Mike, yes, I believe it can be ignored. Your dataset is quite large for SC3, remember it's an old horse!