#> Loading required package: flowCore #> Loading required package: ncdfFlow #> Loading required package: RcppArmadillo #> Loading required package: BH home_dir "FCS_BCE/SEB/Specimen_001_A1_A01_SEB.fcs" #> "QC_FCS/Specimen_001_A1_A01_SEB_HQ.fcs" ws File location: C:/Users/brade/Desktop/reprex_CytoML2/20210121 Workspace_reprex.xml #> #> Groups in Workspace #> Name Num.Samples #> 1 All Samples 1 #> 2 test 1 gs A GatingSet with 1 samples For details, please read the section #> titled "The cytoframe and cytoset classes" in the package vignette: #> #> vignette("flowWorkspace-Introduction", "flowWorkspace") #> As part of improvements to flowWorkspace, some behavior of #> GatingSet objects has changed. I would like to be able to tweak the matrix occasionally in FJ-10, but I can't really do that here. When I go into the compensation window in FJ-10, FJ doesn't recognize the parameters in the compensation matrix as being in the samples: However, there is sometimes a need to tweak our compensation matrices to get the compensation just right. The data look great in FJ-10, reproducing exactly as things were in FJ-9.
use gh_apply_to_cs to apply gating, compensation, transformation to the cleaned sample(s).import cleaned data fcs files as cytoset.While I am doing this migration I decided to use the flowAI package to produce cleaned versions of all the FCS files. Since FJ-9 is becoming obsolete, I am using the cytoverse packages to move the analysis to FJ-10. I am using cytoverse packages to help with analysis of old flow data, which has been partially gated in Flowjo 9.
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