Do we need to remove the "experimentally measured" PE column before clustering?

[denvercal1234GitHub]

Hi there,

Thank you for the tool!

I merged all the FCS files together then do clustering. So in my merged data frame, there will be a column of experimentally-measured PE. But as expected, this column would contain measured PE staining for different markers depending on which well the cells belong to.

It is a bit silly, but I was wondering if we would need to remove this column containing data of experimentally measured PE channel, before we do the clustering? I was concerned if we included this column, it would skew the clustering as PE data in this column are of different markers?

Thank you again for your help!