Hello,

I've been trying to follow the Chromium Single Cell Multiome tutorial, but I'm having some issues with Seurat when I get to the Normalization part:

> seurat <- NormalizeData(seurat, 
                        normalization.method = "LogNormalize", 
                        assay = "RNA")

Error in vapply(X = keyed.objects, FUN = function(x) { :
values must be length 1,
but FUN(X[[1]]) result is length 0 

I haven't found a workaround yet, but the error seems to be due to some incompatibility with SeuratObject (my error has been reported by other users here) and occurs running both the Normalization of RNA and ATAC (which rely on Signac and Seurat, respectively) and Variable Feature Selection (which uses Seurat functions) steps in the tutorial.

Just FYI, I have tried to create the seurat object from the tutorial again using SeuratObject v4.0.4, as suggested in the thread, but it doesn't seem to work.

Just thought I'd report it here in case there is a quick solution (perhaps providing a working seurat object for download?).

Best,

Ángeles

On line 366 in the section Correlate factors with covariates there seems to be a typo.

"We see that Factor 4 is strongly associated with the number of expressed genes per cell and the Factors 1 and 7 are associated with the number of accessible peaks per cell"

But the plot seems to indicate the opposite. Unless I misunderstood the plot entirely, which could happen)

I'd make a PR, but seems it's better for you to regenerate the HTML yourself.