Closed wangzhenzZ closed 5 months ago
I figured out that I might be having trouble at this step: scaleNotCenterFast(t(object@norm.data[[i]][object@var.genes, ]))
, so I modified the code: scale(t(object@norm.data[[i]][object@var.genes, ]), center = FALSE, scale = TRUE)
. This allowed the function to run successfully.
I have two questions:
The overall idea is that we divide each row of a dataset by the value: sqrt( sum(square of the row) / (ncol-1) ), and then use the transpose. And yes, scale(t(object@norm.data[[i]][genes, ]), center = FALSE, scale = TRUE)
is exactly equivalent.
For the error, can you make sure that all the var.genes can be found in your norm.data? For example:
sapply(object@norm.data, function(nd) all(object@var.genes %in% rownames(nd)))
Thank you for creating this useful package! I'm using rliger_1.0.0 in R 4.2.0. I'm trying to integrate multiple scRNA-seq datasets following the provided vignette.
The
scaleNotCenter()
took about 2 hours to run, and then I got the above error message. Could you please advise what I could do to troubleshoot and fix this issue? Any suggestions would be greatly appreciated.