improving running time of runNMF
1
0
Entering edit mode
@lirongrossmann-23954
Last seen 3.8 years ago

Enter the body of text here

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 • 1.0k views
ADD COMMENT
0
Entering edit mode
Aaron Lun ★ 28k
@alun
Last seen 2 hours 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.

ADD COMMENT

Login before adding your answer.

Traffic: 510 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6