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?

enter image description here FSC-A vs FSC-H: plotted only negative FSC-A values

enter image description here SSC-H vs FSC-A: red points indicate negative FSC-A values

  • $\begingroup$ Why did you delete the SSC-H plot? Also, yould you post the corresponding SSC-A/-W FSC-W plots? $\endgroup$
    – bukwyrm
    Commented Apr 27, 2018 at 13:21
  • $\begingroup$ @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. $\endgroup$
    Commented Apr 27, 2018 at 13:52

1 Answer 1


This is probably a matter of calibration. If this is not the raw data (actual voltage curves), look at that.

As an area below 0 is not possible, it has to be a calibration issue, either in the machine, or in the software.

the -H plots are about the maximum height of the voltage spike in the side or forward light detector, while the -W plots are about the width (using some definition of flank-detection, so variation prone). The area is also computed in various ways: using something like (H*W)/c (with c something like 2) or with an actual computation of the area of the spike, but again this has all kinds of predefinitions in it (what's the beginning/end of a spike, what's the background-level, ...) Some of these predefinitions you can alter in software, some are hardcoded or even part of the functionality of the hardware, so it might be easy to impossible to get rid of the negative values.

The FSC-H values corresponding to the FSC-A values are in your plot, and positive, so the most obvious solution (a bad algorithm that calculated Area as Height times Width times Magic and did not account for negative Heights (which depending on spike definition, you might get)) is out.

  • $\begingroup$ So basically there is some unknown bad algorithm that is responsible for this. Should I consider FSC-H as the reliable estimate and retain these points for further analysis or discard them? As I mentioned in the other comment, removing these points does not change the SSC or FITC distribution. $\endgroup$
    Commented Apr 27, 2018 at 14:02

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge you have read our privacy policy.

Not the answer you're looking for? Browse other questions tagged or ask your own question.