# What are negative FSC-A values in flow cytometry data?

I did flow cytometry analysis of E. coli cells 7 hours post inoculation (1% overnight culture in 3ml).

I am analysing the FCS3.0 files using the flowCore package in R. I observe that FSC-A has negative values in some events, although the corresponding FSC-H values were all positive. These points comprised just a minor fraction of the data (~250/10000 in this case). The FSC voltage was set at 788V and the threshold flow rate was 5000-10000 events/sec.

What do these negative values mean?

FSC-A vs FSC-H: plotted only negative FSC-A values

SSC-H vs FSC-A: red points indicate negative FSC-A values

• Why did you delete the SSC-H plot? Also, yould you post the corresponding SSC-A/-W FSC-W plots? Apr 27, 2018 at 13:21
• @bukwyrm well, what I claimed in the image that I posted wasn't really true. I don't have the -W data. I tried to see if there is any correlation but the only thing that I could find is that these negative FSC-A points have low SSC-H but removing these points from the total data does not change the distribution of the latter. Apr 27, 2018 at 13:52