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DillonHammill / CytoExploreR

Interactive Cytometry Data Analysis
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Guidance on Editing Compensation Matrix from FACS DIVA pre-compensated FCS Files #191

Closed tiagobrc closed 9 months ago

tiagobrc commented 9 months ago

Issue Description:

Hello @DillonHammill,

I have been using your R package for flow cytometry data analysis and have encountered some challenges related to the compensation matrix when dealing with already compensated FCS files.

Briefly describe what you hope to achieve:

I would like to extract the compensation matrix from FCS files. Or do I have to export uncompensated data? I aim to edit this compensation matrix if necessary.

Outline the steps taken to attempt to reach this goal:

While the package documentation provides a general understanding of flow cytometry analysis, I couldn't find explicit steps or methods for dealing with the compensation matrix when using pre-compensated FCS files.

Running the package works just fine but I would like to tweak the matrix.

Best regards,

Tiago

DillonHammill commented 9 months ago

You can remove the applied compensation after reading the files using gs <- cyto_compensate(gs, remove = TRUE). Then pass the GatingSet to cyto_spillover_edit().

cyto_spillover_edit() will automatically extract the spillover matrix from your samples if it isn't supplied manually to spillover.

tiagobrc commented 9 months ago

This is helpful! Thanks!