Quite low accuracy using index cluster

[Kevis9]

Hi, I am trying to use scmap to predict unlabeled datasets (let's call query) based on reference dataset. I use scmap index cluster followed by this vignette. The prediction accuracy is quite low, about only 0.007. However accuracy produced by scmapCellindex is quite high, about 0.91. I checked other papers which also used scmap to predict labels, it seems like indexCluster function work well at their experiment. I don't know whether there is any mistake in my code.

I checked prediction results, there lots of "unassigned" label in it. Can you give an example of how to use scmap index cluster to do prediction work based on reference datasets projecting to query dataset ?

[mhemberg]

Not sure if you have already tried this, but the best way of getting rid of "unassigned" labels is to lower the "threshold" parameter (which exists for both versions of scmap). Not really sure why one method does not run into this problem, but I would suggest gradually lowering it from the default of 0.7.

Hope this helps.

[Kevis9]

Thank you. That's very helpful.