How to use FindConservedMarkers against a standard control?

[alexwskh]

Hello everyone, hoping to get some support here.

I have an integrated cell dataset done with SCTransformation and CCA integration, consisting of four slightly different experimental conditions and one control condition (currently). The clustering looks nice, and I am able to do some FindMarkers analysis of the four experiments versus control, which is great. I am seeing that sometimes, genes that are really strong in one experimental condition are picked up as a marker for the pooled analysis, which makes sense, but I'd like to look for better common markers.

It's my assumption that FindConservedMarkers can be used in a situation like this, testing for Markers that are shared between the groups. So let's say I have cluster 5, with contributions from 4x experimental and 1x control. I want to FindConservedMarkers the four experimental against the control.

When I try to employ it this way, it is looking for a control condition in each of the experimental groups. What is the proper way to go about this?