Tolerance in panel design
I have a basic question when it comes to panel design, especially with regards to 'tolerance'. When designing a panel with ~40 antibodies, I find it impossible to make a 'clean' panel. I want to ask the users here, based on your experience, how much spillover can you tolerate? Is it essential that the spillover does not cross the particular antibody's 'tolerance' value? The general guidelines seem to be to match marker abundance with appropriate bright/dim metal, try to place mutually exclusive markers in more dirtier channel etc. But following all these guidelines often leads to many custom conjugations (which seems to further deter users from adopting cytof, since we don't maintain an antibody bank). Is this just the way it rolls or am I missing something obvious?
Thanks for your input,
Santhosh