Gene names in nmf basis

[liron27]

Hello

I am trying to run runNMF from scater and would appreciate your help.

I have a seurat object that I converted to SingleCellExperiment using:

object.sce<-as.SingleCellExperiment(object.seurat)

Then I run runNMF:

res<- runNMF(object.sce,ncomponents= 10, ntop = 1000)

I get the nmf.out via reducedDim

nmf.out <- reducedDim(res,"NMF")

and to get the basis

nmf.basis<-attr(nmf.out,"basis")

The problem is: the nmf.basis rows correspond to the genes but they are not annotated (see picture attached). I don't know the order of the genes (it takes the top 1000 variable genes).

Any help? Thanks, Liron

[alanocallaghan]

Sorry just circling around to this now. Your picture seems to be missing

[alanocallaghan]

A fix is on the way to bioc devel