I am trying to get familiar with SingleR and using it to annotate my human spinal cord data set. However, although I am pretty sure that the cells I am trying to analyse are oligodendrocytes (based on the expression of Oligodendrocytes-specific genes), SingleR failed to annotate cells.
I am using following code:
You are presenting the orig.ident, not the cell annotations. Your input for orig.ident is NA.
Just remove labels = singler$meta.data$orig.ident for the SingleR.PlotTsne call and it should work
Hi Dvir,
Thank you for developing such a useful tool!
I am trying to get familiar with SingleR and using it to annotate my human spinal cord data set. However, although I am pretty sure that the cells I am trying to analyse are oligodendrocytes (based on the expression of Oligodendrocytes-specific genes), SingleR failed to annotate cells. I am using following code:
out$p
The result is:![SingleR](https://user-images.githubusercontent.com/49162517/63258310-1248b980-c27c-11e9-83c0-395450df2d3a.jpeg)
Am I doing something wrong, or something else is problem?
Any help will be appreciated.
Kind regards, Amel Zulji