Open atermanini opened 5 years ago
Hi,
I am trying to merge datasets, my code follow the tutorial and worked fine with other datasets, but with those samples I got this error:
Error in irlba(A = t(x = object), nv = npcs, ...) : starting vector near the null space Calls: <Anonymous> ... RunIntegration -> RunPCA -> RunPCA.default -> irlba
Anyone can help me?
I am using the last Seurat v3 from develop branch.
Thanks very much, Alberto
Merging dataset 7 into 2 Extracting anchors for merged samples Finding integration vectors Finding integration vector weights 0% 10 20 30 40 50 60 70 80 90 100% [----|----|----|----|----|----|----|----|----|----| **************************************************| Integrating data Merging dataset 2 7 into 5 Extracting anchors for merged samples Finding integration vectors Warning in irlba(A = t(x = object), nv = npcs, ...) : fast code path error starting vector near the null space; re-trying with fastpath=FALSE. Error in irlba(A = t(x = object), nv = npcs, ...) : starting vector near the null space Calls: <Anonymous> ... RunIntegration -> RunPCA -> RunPCA.default -> irlba Inoltre: Warning messages: 1: In CheckDuplicateCellNames(object.list = object.list) : Some cell names are duplicated across objects provided. Renaming to enforce unique cell names. 2: In `[<-.data.frame`(`*tmp*`, , 2, value = list(1126L, 1134L, 1135L, : provided 8463 variables to replace 1 variables 3: In `[<-.data.frame`(`*tmp*`, , 2, value = list(1777L, 1777L, 1778L, : provided 19214 variables to replace 1 variables Esecuzione interrotta
I have no idea. This is something related to Seurat and not SingleR. Try creating Seurat objects of these samples and merge them, maybe you can detect the issue.
Best, Dvir
Hi,
I am trying to merge datasets, my code follow the tutorial and worked fine with other datasets, but with those samples I got this error:
Anyone can help me?
I am using the last Seurat v3 from develop branch.
Thanks very much, Alberto