Sorry if this is a beginner's question or that it has been asked (and answered) before, but I would just like to know: what is the use of a positive control (eg: constitutively-expressing GFP) and a negative control (eg: no fluorophore or constitutively-expressing RFP - irrelevant fluorophore) in flow cytometry?
Background: I'm a Master student who just started some experiments with flow cytometry. My sample is a bacterium (Bacillus subtilis) that expresses GFP when induced by an extracellular stimulus. I have positive and negative controls (as described above) using the same bacterium and I'm wondering, what's the use of these controls in flow cytometry?
Correct me if I'm wrong, but negative control (no fluorophore or with irrelevant fluorophore) is to show the background auto-fluoroscence and also show where is the population of cells in my dot-plot so that I can gate only my cells while ignoring other pieces of background stuff (eg dust). Positive control is to show my cell population as well? Because I'm only using one color for detection in my experiment, the positive control cannot be for compensation reasons, right?
So can anyone tell me the uses of these controls?