Thu Mar 23, 2017 8:59 pm by mleipold
Hi Naeem,
I don't really have a good answer for your question....it's not something I've investigated closely.
You should be able to try distributing the zeroes in some fashion, between -1 and 0 as you discuss. There's also a re-processing step you can do: if you have the FCS file, you can go into FCS Processing and play with the Gaussian Negative Half-Zero Randomization.
This is normally unselected ("off"). In CyTOFv1 software, it was accessible in User Mode. In Helios, it's visible in all modes, but only clickable in Service Mode. I'm not sure about CyTOFv2 software, and I don't have one handy to check. I'm sure there are ways to do this in R or some other language too.....
In short, this allows you to take your zeroes (and only your zeroes) and randomize them around zero, according to a Gaussian distribution. You have the ability to play with the shape of the distribution by changing the Sigma and the Power Parameter. I have attached a couple slides from several years ago when I looked at this.
**Personally, I don't think this is a good idea, as it's injecting noise into your data for what I consider to be only aesthetic reasons (ie, make it look like Flow data). And, depending on the wifth of your peak-shape, you could wind up losing some resolution against Dim populations.
However, for the purposes of testing whether the pile-up on Zero is causing your viSNE "wispiness", it might be useful.
Mike