Mon Dec 09, 2019 7:26 pm by jimbomahoney
OK, after much testing and tweaking, I think I've come up with a method to gate the beads (i.e. remove them).
The new version on GitHub has two significant changes:
1) Removing Beads is now optional.
2) If bead removal is enabled (default), the script will examine each bead channel.
3) Whichever channel has the clearest separation between the cells (low intensity) and beads (high intensity), it will use that Channel to set the cut-off appropriately.
This should work even when markers are used in one or more of the bead channels.
It works on all the datasets I have, some of which have markers in most of the bead channels.
However, I can see a possibility of the bead removal failing, or not working properly, if ALL the bead channels are "noisy" as a result of being used for cell markers. Hence why the bead removal is now optional.
UPDATE 3rd March 2020 - OK, the new version now also asks the user which bead channel(s) they want to use. Ideally, these would not have been used for markers.
Last edited by
jimbomahoney on Tue Mar 03, 2020 3:16 pm, edited 1 time in total.