Is there a recommended way of extracting the log fold change when using scran's findMarkers function? I understand the reason why AUC is used here but AUCs is nothing that I can present to my PI or wetlab co-workers. Manually calculating lfc based on the logcounts or simply running ttest-based findMarkers and lifting over the lfcs is simple enough, but I would like to have confirmation that findMarkers is not doing anything internally that changes the lfcs from the values I'd get by naive/custom calculation. Thanks you!

I would like to have confirmation that findMarkers is not doing anything internally that changes the lfcs from the values I'd get by naive/custom calculation.

Yes.

You may also find the multiMarkerStats() function helpful, depending on how you want to do the lift-over.