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flowWorkspace
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gs_pop_get_stats MFI returning inf values #352

Closed alexheubeck closed 3 years ago

alexheubeck commented 3 years ago

Hi @jacobpwagner,

I updated flowWorkspace to 4.1.13, and the gs_pop_get_stats function is now returning inf MFI values for all populations that aren't the root node.

This is the line I'm using: mfi <- as_tibble(gs_pop_get_stats(gs,type = pop.MFI,inverse.trans=TRUE))

And this is the table it's returning:

sample pop CD3 CD45 CD15 CD45RA CD14 CD8 CD11c CD25 (IL2Ra) CD4 Viability CD16 CD123 (IL3Ra) CD127 (IL7Ra) IgD CD304 CD141 CD11b CD19 CD27 abTCR CD34 CD197 (CCR7) CD38 CD56 HLA-DR
B011_PS1_FSQBAZ0BC00-01.fcs root 25616.5928 291037.172 3352.07068 27206.7695 1312.95978 7756.07837 1150.63928 860.526917 3848.13599 4028.37671 3093.64832 1228.84186 2012.44177 1236.0426 1414.28009 1399.2337 1728.54285 524.656433 3486.40161 38723.1523 1229.11938 2212.78052 5914.71167 909.916199 2829.16467
B011_PS1_FSQBAZ0BC00-01.fcs /Cells Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf
B011_PS1_FSQBAZ0BC00-01.fcs /Cells/Singlets-H Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf
B011_PS1_FSQBAZ0BC00-01.fcs /Cells/Singlets-H/Singlets-W Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf
B011_PS1_FSQBAZ0BC00-01.fcs /Cells/Singlets-H/Singlets-W/Cleanup Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf
B011_PS1_FSQBAZ0BC00-01.fcs /Cells/Singlets-H/Singlets-W/Cleanup/Non-viable Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf
B011_PS1_FSQBAZ0BC00-01.fcs /Cells/Singlets-H/Singlets-W/Cleanup/Viable Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf Inf

It's the same thing for the other files in the gating set. I haven't changed anything else in the script since it was working correctly, so just seeing if something changed with that function.

Thanks,

Alex   


R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] devtools_2.3.2           usethis_1.6.3            gridExtra_2.3            colorRamps_2.3           tidyr_1.1.2              dplyr_1.0.2              tibble_3.0.4             scales_1.1.1            
 [9] cytolib_2.1.20           CytoML_2.1.14            data.table_1.13.2        flowDensity_1.23.0       ggcyto_1.17.0            ggplot2_3.3.2            ncdfFlow_2.35.1          BH_1.72.0-3             
[17] RcppArmadillo_0.10.1.0.0 flowCore_2.1.4           flowWorkspace_4.1.13     openCyto_2.1.2
jacobpwagner commented 3 years ago

@alexheubeck , thanks, you caught a pretty nasty bug resulting from some necessary changes for the flowFrame->cytoframe transition that we hadn't yet made. It's fixed in https://github.com/RGLab/flowWorkspace/commit/c816cf509936a892971004b5f960de2b4650ed59, so hopefully everything should be good after re-installing flowWorkspace from GitHub. Otherwise, I'm merging that fix over to Bioconductor so it should be available there in flowWorkpsace version 4.1.14 in a couple of days.

alexheubeck commented 3 years ago

Thanks @jacobpwagner, much appreciated. I think my scripts are working properly again. Thanks again for the fast response!

jacobpwagner commented 3 years ago

Sounds good. I'm going to close this then as this problem seems pretty self-contained and now fixed. But feel free to re-open it if you run in to this again somehow.