Undefined column requested Error

[rwbaer]

Briefly describe what you hope to achieve: -I'm trying to apply a 2 channel compensation to a gating set

Outline the steps taken to attempt to reach this goal (paste code below): The spill matrix was created in separate source file and save in Spillover-Matrix.csv

I then created a gating set and tried to apply the compensation, but got an undefined column error that I don't understand.

# load in data from "Samples" folder
gs <- cyto_setup("Samples",
                 gatingTemplate = "Samples-gating.csv")

# Show us what we have
cyto_channels(gs)
cyto_markers(gs)
cyto_fluor_channels(gs)

# Apply compensation
gs <- cyto_compensate(gs,
                      spillover = "Spillover-Matrix.csv")

The resulting console output and error is shown below. Not sure where I'm going wrong. Include any associated screenshots or images here:

[DillonHammill]

@rwbaer, thanks for reporting this. Looks like a bug in cyto_compensate() - it is expecting your spillover matrix to contain all the flourescent channels in your samples. I will push a fix later today.

[DillonHammill]

@rwbaer, this should now be fixed.

Please pull down the latest version from GitHub and try again: devtools::install_github("DillonHammill/CytoExploreR")

[rwbaer]

This seems to be working now. Thanks.