I suspect CyTOF FCS files contain multiple datasets each (presumably randomized and non-randomized expression matrix) and I am wondering how to identify them? How to confirm they're indeed in there and, if yes, extract them? I tried importing the FCS file with
dataset = 1 and
dataset = 2, but resulting flowFrame looks the same. Is the syntax correct? Intuitively, this would suggest there are no multiple datasets, but how to confirm this, as other procedures suggest they're there (for instance, reading in the file into flowJo and re-exporting it creates a fully functional file with less than half the size of the initial one)?
I welcome any feedback I can get on this.
Thanks and best,