You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
Currently analysing a 10X Multiome dataset. When I run FindMarkers() on an ATAC assay with custom peaks using DESeq2 I get an error back. Appreciate if someone here could teach me how to understand and troubleshoot this.
Code used:
# https://github.com/satijalab/seurat/discussions/7763
# add 1 so that DESeq2 will run
so@assays$customPeakList$counts <- as.matrix(so@assays$customPeakList$counts+1)
# FindMarkers()
markers <- FindMarkers(so, ident.1 = "Control", ident.2 = "Knockout",
group.by = "sampleSource",
assay = "customPeakList",
test.use = "DESeq2")
Resulting error message:
converting counts to integer mode
gene-wise dispersion estimates
mean-dispersion relationship
Error in lfproc(x, y, weights = weights, cens = cens, base = base, geth = geth, :
newsplit: out of vertex space
In addition: There were 17 warnings (use warnings() to see them)
Hi, this error occurs if every single feature contains at least one zero, so it does indicate sparsity. Can you describe more about your data here? How did you pseudobulk here? If you look at some entries of so@assays$customPeakList$counts, does it seem very sparse across the board or are there a couple of particular outlier samples causing the sparsity?
Currently analysing a 10X Multiome dataset. When I run FindMarkers() on an ATAC assay with custom peaks using DESeq2 I get an error back. Appreciate if someone here could teach me how to understand and troubleshoot this.
Code used:
Resulting error message:
sessionInfo:
The text was updated successfully, but these errors were encountered: