I have a 10X single cell experiment that has ~8000 cells in it. When I feed it into SingleR, I get cell type predictions for only about 800 cells. I have not noticed this in other experiments. Now this experiment has other aspects besides gene expression and it seems to be behaving strangely there as well.
My hypothesis is that something went wrong in the lab. But it has exposed behavior in SingleR that has surprised me. SingleR does at times return output for cells that it does not feel comfortable labeling. They end up getting their labels removed during the "pruning" stage. This made me expect to get SOMETHING for every cell I give it. Even if the output is equivalent to "UNLABELED".
My question is: Should I expect an "answer" for every cell I give to SingleR? Or if the first stage of the process fails to find a similar expression profile in the reference(s) does the code drop that cell from the output?