# flowCore’ version 1.38.1
Steps to reproduce:
1. Read an .fcs file created with a BioRad S3 cell sorter using f <- read.FCS(.)
# Names of in flowFrame
names(f@description)
[1] "FCSversion" "$BEGINANALYSIS" "$ENDANALYSIS"
[4] "$BEGINDATA" "$ENDDATA" "$BEGINSTEXT"
[7] "$ENDSTEXT" "$NEXTDATA" "$DATATYPE"
[10] "$MODE" "$PAR" "$BYTEORD"
[13] "$TOT" "$SYS" "$CYT"
[16] "$CYTSN" "$INST" "$P1N"
[19] "$P1S" "$P1B" "$P1R"
[22] "$P1E" "$P1G" "$P1CALIBATION"
[25] "$P2N" "$P2S" "$P2B"
[28] "$P2R" "$P2E" "$P2G"
[31] "$P2CALIBATION" "$P3N" "$P3S"
...
[145] "$P21G" "$ETIM" "$BTIM"
[148] "$DATE" "$SPILLOVER" "FILENAME"
[151] "transformation" "flowCore_$P1Rmax" "flowCore_$P1Rmin"
[154] "flowCore_$P2Rmax" "flowCore_$P2Rmin" "flowCore_$P3Rmax"
[157] "flowCore_$P3Rmin" "flowCore_$P4Rmax" "flowCore_$P4Rmin"
[160] "flowCore_$P5Rmax" "flowCore_$P5Rmin" "flowCore_$P6Rmax"
[163] "flowCore_$P6Rmin" "flowCore_$P7Rmax" "flowCore_$P7Rmin"
[166] "flowCore_$P8Rmax" "flowCore_$P8Rmin" "flowCore_$P9Rmax"
[169] "flowCore_$P9Rmin" "flowCore_$P10Rmax" "flowCore_$P10Rmin"
[172] "flowCore_$P11Rmax" "flowCore_$P11Rmin" "flowCore_$P12Rmax"
[175] "flowCore_$P12Rmin" "flowCore_$P13Rmax" "flowCore_$P13Rmin"
[178] "flowCore_$P14Rmax" "flowCore_$P14Rmin" "flowCore_$P15Rmax"
[181] "flowCore_$P15Rmin" "flowCore_$P16Rmax" "flowCore_$P16Rmin"
[184] "flowCore_$P17Rmax" "flowCore_$P17Rmin" "flowCore_$P18Rmax"
[187] "flowCore_$P18Rmin" "flowCore_$P19Rmax" "flowCore_$P19Rmin"
[190] "flowCore_$P20Rmax" "flowCore_$P20Rmin" "flowCore_$P21Rmax"
[193] "flowCore_$P21Rmin" "GUID"
# Now try to access this data and note a strange parsing problem
# i.e., some fields seem to have extra $ character and require backwards apostrophe " ` "
# It seems this is not intended, but I don't know if this is a "file reading" or "file writing" problem"
# It certainly is in net a "file parsing" problem
# Example
> f@description$DATE
NULL
# But with extra $ and back single quote
> f@description$`$DATE`
[1] "17-May-2016"
# on the other hand some things work as expected
> f@description$GUID
[1] "2016-05-17 b16.fcs"
> f@description$FILENAME
[1] "./fullFCS/2016-05-17 b16.fcs"
# Another broken one:
> f@description$SPILLOVER
NULL
# The oddball fix
> f@description$`$SPILLOVER`
FL1-AREA FL2-AREA FL3-AREA FL4-AREA
[1,] 1 0 0 0
[2,] 0 1 0 0
[3,] 0 0 1 0
[4,] 0 0 0 1
Question: Is this a flowCore parsing problem or an S3 Cell Sorter writing problem? And obviously, is there a way to improve this parsing behavior?
Thanks,
Rob Baer
Professor of Physiology
AT Still University of Health Sciences
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flowCore’ version 1.38.1 running on Windows 10 in US locale
It could be important that I'm running inside RStudio 0.99.893
-------------------------------------------------------------------------------------
> sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
other attached packages:
[1] flowViz_1.36.2 lattice_0.20-33 flowCore_1.38.1 sfsmisc_1.1-0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.5 matrixStats_0.50.2 mvtnorm_1.0-5
[4] corpcor_1.6.8 rrcov_1.3-11 MASS_7.3-45
[7] grid_3.3.0 stats4_3.3.0 pcaPP_1.9-60
[10] KernSmooth_2.23-15 graph_1.50.0 hexbin_1.27.1
[13] latticeExtra_0.6-28 robustbase_0.92-5 RColorBrewer_1.1-2
[16] tools_3.3.0 Biobase_2.32.0 DEoptimR_1.0-4
[19] parallel_3.3.0 BiocGenerics_0.18.0 cluster_2.0.4
[22] IDPmisc_1.1.17
