How to visually assess whether to increase IT_limit/MAD from QC result plots?

[denvercal1234GitHub]

Hi there,

Thanks for the package.

I have the following plots generated with default values of IT_limit and MAD for a sample having 64469 events.

Would you mind helping me interpret the results and plots below as an example of how we should use these report and plots and summary heatmap to decide whether we should increase or decrease IT_limit and MAD arguments?

Thank you for your help.

PeacoQC_report.txt:

Filename	Nr. Measurements before cleaning	Nr. Measurements after cleaning	% Full analysis	Analysis by	% IT analysis	% MAD analysis	% Consecutive cells	MAD	IT limit	Consecutive bins	Events per bin	Increasing/Decreasing channel
channelFCS_FileID_P1_B7_CD107A.fcs	64469	63969	0.775566551365773	all	0.775566551365773	0	0	6	0.55	5	500	No increasing or decreasing effect

PeacoQC_plots:

With the same values for MAD and IT_limit, this sample had events shaded by MAD:

Heatmap of PeacoQC_report.txt