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Exporting fcs files from FlowJo to cyt(viSNE)

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Posts: 6

Joined: Mon Dec 02, 2013 11:51 am

Post Tue Feb 18, 2014 7:00 am

Exporting fcs files from FlowJo to cyt(viSNE)

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?



Posts: 4300

Joined: Fri Nov 01, 2013 5:30 pm

Location: Stanford HIMC, CA, USA

Post Tue Feb 18, 2014 4:28 pm

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

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.

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