Page 1 of 1

Exporting fcs files from FlowJo to cyt(viSNE)

PostPosted: Tue Feb 18, 2014 7:00 am
by rrotkopf
Hello all,

I've encountered a problem when exporting gated created in FlowJo as fcs files to cyt.
The values get read wrong and the graphs are all skewed. For instance, Event length which is <200 for all the data set, gets read as values of 10,000+.

Has anyone else encountered this problem?

Re: Exporting fcs files from FlowJo to cyt(viSNE)

PostPosted: Tue Feb 18, 2014 4:28 pm
by mleipold
I haven't played with viSNE, so I don't have direct experience with this.

However, if you're exporting a new FCS file from FlowJo (which version?), I assume you've already gated down to Live Intact Singlets (ie, gated out debris, doublets, and dead cells) so you can do viSNE on true cells.

If so, de-select Ir191, Ir193, Time, and Cell_length/Event_length, and your Live-dead from the parameters to export, and see whether that makes a difference. I know Cell/Event Length can sometimes be displayed wonky, depending on how the scaling from the CyTOF FCS file gets read by even FlowJo, let alone SPADE or viSNE.