I'm trying to use the OpenCyto platform to streamline our FACS analysis. I've generated a GatingSet from a FlowJo .acs archive - incidentally for other users who've experienced similar problems with .wsp files, I've found that if the workspace is bundled together into an archive then
parseWorkspace seems to work.
I then generated a template file using the
templateGen function. After modifying the gating method column in the csv template file I try to import the template back using the
gatingTemplate function, whereby I get an
Error in .validity_check_alias(this_row[, alias]) : Q4: CD4-FITC-H- , CD8-PE-H-contains illegal character: |,&,:,/
I think the error is self descriptive, i.e. it's because of the colon character but it would seem to me that
a) quite many FlowJo workspaces will have some sort of quadrant gate, which will have this type of syntax
b) if I rename the aliases in the template I get
Error in .cpp_setNodeName(x@pointer, sampleNames(x), y, value) : Q1: CD4-FITC-H- , CD8-PE-H+ not found!
Is there a workaround for this?
Also, I'm struggling somewhat to figure out what gating methods to use in the template file. Is there any documentation on this? That would be much appreciated.