Hello,

I have very recently become familiar with Bioconductor, FlowJo, and Flow Cytometry in general, so forgive me if my questions are simple. I am trying to load in FCS files that have not been gated, with the purpose of counting monocytes labeled with HLA-DR. I have loaded the FCS files into FlowJo and saved the workspace as a .wsp file, and have managed to open the workspace in R. I have two questions however.

1) When calling parseWorkspace(ws), there are no groups of samples listed. However, if I add a gate to a single FCS file in FlowJo, then the workspace will show groups when calling the parseWorkspace command, however only the groups that the gated file belongs to. Why is this, and how do I parse all of my ungated files in my workspace?

2) How would I count the number of monocytes labeled with HLA-DR?

I would really appreciate help, as I am a new student doing research and am struggling a bit.