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?
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!