EmbedSWNE fails

[bobermayer]

Hi,

I have a large dataset with more than 20k cells. trying

swne.embedding <- EmbedSWNE(nmf.scores, snn, alpha.exp=alpha.exp, snn.exp=snn.exp, n_pull=3, dist.use='IC')

I get the following error:

Error in SNN %*% t(H) : 
  Cholmod error 'X and/or Y have wrong dimensions' at file ../MatrixOps/cholmod_sdmult.c, line 90

although the dimensions should match (after subsetting snn to the relevant cells):

dim(nmf.scores)
[1]     4 20565
dim(snn)
[1] 20565 20565

any ideas what's wrong here?

thanks!

[yanwu2014]

Ah that might be because in certain corner cases we need to filter the NMF matrix for columns with all zeros, which may cause the dimensions to be off. I've pushed an update to SWNE. Can you reinstall the package and see if you're still getting the bug?

[bobermayer]

yes, thanks a lot, that fixed it!