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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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Error in gatingset_to_flowjo(gs, outfile) #59

Closed mehrnoushmalek closed 5 years ago

mehrnoushmalek commented 5 years ago

Hello,

I updated my flowWorkspace, Cytolib, CytoML packages, and I get the error of : Error in getSpilloverMat(gh) : trying to get slot "spillover" from an object of a basic class ("matrix") with no slots When I try getCompensationMatrices(gs[[1]]), I get my comp matrix, but not an spillover object ( where the code tries to access mat <- compobj@spillover). I looked at the code and my gh@compensation returns back a list that has compensations of all my samples. I couldn't find anything in the man page that got changed with the new version, that should be added. Is there anything that I should add to the gatingSet to avoid this error? I don't have the problem with the older version of flowWorkspace( before changing functions name ,...).

p.s. I apply the compensation on the gs.

mikejiang commented 5 years ago

This may be related to the changes from RGLab/flowWorkspace@bc3eab66e63ed67a9d70a14699e3688225fd3752 I will try to reproduce the error and find a fix for you.

jacobpwagner commented 5 years ago

I'm not sure it is related to RGLab/flowWorkspace@bc3eab6, as I can reproduce after reverting to just before that, but only when compensating a GatingSet with a simple spillover matrix as opposed to a compensation object. As you highlighted, @mehrnoushmalek , it looks like the code for gatingset_to_flowjo() currently assumes that the compensation slot for the GatingSet is a compensation object and not a matrix. I'll get a fix up pretty soon.

jacobpwagner commented 5 years ago

@mehrnoushmalek , 1386968 should fix it. But if that's not the case, let me know and I'll re-open this.