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RGLab / CytoML

A GatingML Interface for Cross Platform Cytometry Data Sharing
GNU Affero General Public License v3.0
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Support for FCS 3.2? #156

Open alefrol638 opened 3 months ago

alefrol638 commented 3 months ago

Dear CytoML Team,

I am trying to import gates from a workspace, which works with FCS files from the new BD software FACS CHORUS. The FCS files are FCS 3.2 and the function gives me the error, that the format is wrong: 

 gs  <- flowjo_to_gatingset(open_flowjo_xml(wsp, sample_names_from="sampleNode"), name = 1,mc.cores = 7,path = <pathToFile>) #flowWorkspace package

Error: This does not seem to be a valid FCS2.0, FCS3.0 or FCS3.1 file

Is there a way to work with this workspace/FCS files?

Thanks!

mikejiang commented 3 months ago

We don't have official support for 3.2 yet, did relax the check in flowcore https://github.com/RGLab/flowCore/pull/263 so that it can be load there, I can do a similar change in cytolib to allow your workspace parsing proceed, but no guarantee it will work if your fcs is not fully compatible with 3.1

alefrol638 commented 3 months ago

all right, I would give it a try

mikejiang commented 3 months ago

https://github.com/RGLab/cytolib/pull/58

mikejiang commented 3 months ago

I pushed the cytolib change to bioconductor develop branch: To trigger the rebuild for CytoML, I bumped its version to 2.15.3 as well