improving running time of runNMF
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@lirongrossmann-23954
Last seen 18 months ago

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Hi, Is there a way to make runNMF from "scater" run faster? It takes a very long time to run compared to other dimensionality rreduction methods.

Thanks

runNMF scater singlecell SingleCellExperiment • 343 views
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Aaron Lun ★ 27k
@alun
Last seen 1 hour ago
The city by the bay

scater::runNMF just defers to the NMF package, which seems to be quite slow compared to, e.g., the usual PCA algorithms. Fiddling with the different method= options doesn't really help, I'm afraid.

We used to use NNLM, which was much faster... but that got kicked off CRAN. If I can find the motivation, I may just transplant the code into scater. Not the best solution, but that's how it is.