Increased decontaminated signals

[Cscharlotte]

Hi there,

Thank you for developing the tools. I am applying decontPro on some 10x ADT data, and I observed an uncommon behavior that for some markers, e.g., CD16, CD8, there were increasing signals for decontaminated compared to original on the density plot. Decontaminated signals for these markers tended to be spikes and had higher density at higher expression level. Curious if you have seen similar behaviors in your testing and any ideas of the potential causes

Thanks you!

[joshua-d-campbell]

Hi @Cscharlotte, thanks for trying out our tool. We have not observed this behavior before. It would help if you could post some of the plots that show the density before and after running the tool (using the "plotDensity" function).

One way that the tool can be tweaked is by adjust the "clustering" parameter. Sometimes using broader cell type clusters is more useful so altering the clustering resolution can help.