flowcore:::read.FCS does not read FCS3.1 correctly
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cahyasu88 • 0
@cahyasu88-21844
Last seen 2.1 years ago

Hi,

I recently received an .fcs file from a newer instrument that uses the newest version 3.1. The flowcore::read.FCS function appears to read the data incorrectly, compared to when the .csv export from FlowJo. Below is the table of the first 10 rows of the values, compared side-by-side between read.FCS and FlowJo output. Note that the same script reads prior versions (3.0) correctly (or to be exact, comparable to that of FlowJo output as an independent platform that I have access to)

No read.FCS.out FlowJo.out 1 679092 403.021 2 679092 11249.600 3 679092 36962.900 4 679092 556.698 5 679092 482.432 6 679092 21408.400 7 679092 89833.200 8 679092 88422.000 9 679092 486.400 10 15360 1.536

I used the default read.FCS function, i.e. except for filename, optional parameters are default. The session info can be found at the bottom. I can also provide the .fcs file. Let me know if there is a way for me to post the .fcs file, I'm new to this forum.

Best regards, Suntara

Session Info:

R version 3.6.0 (2019-04-26) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Red Hat Enterprise Linux

Matrix products: default BLAS: /lrlhps/apps/R/qualified/R-3.6.0/lib64/R/lib/libRblas.so LAPACK: /lrlhps/apps/R/qualified/R-3.6.0/lib64/R/lib/libRlapack.so

locale: [1] LCCTYPE=enUS.UTF-8 LCNUMERIC=C LCTIME=enUS.UTF-8 LCCOLLATE=enUS.UTF-8 LCMONETARY=enUS.UTF-8 LCMESSAGES=enUS.UTF-8
[7] LC
PAPER=enUS.UTF-8 LCNAME=C LCADDRESS=C LCTELEPHONE=C LCMEASUREMENT=enUS.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] flowCore_1.50.0

loaded via a namespace (and not attached): [1] pcaPP1.9-73 Rcpp1.0.1 DEoptimR1.0-8 compiler3.6.0 pillar1.4.0 plyr1.8.4 prettyunits1.0.2 tools3.6.0
[9] pkgbuild1.0.3 lattice0.20-38 tibble2.1.1 gtable0.3.0 pkgconfig2.0.2 rlang0.3.4 graph1.62.0 cli1.1.0
[17] rstudioapi0.10 parallel3.6.0 mvtnorm1.0-10 xfun0.7 loo2.1.0 gridExtra2.3 cluster2.0.8 dplyr0.8.1
[25] knitr1.23 stats43.6.0 grid3.6.0 tidyselect0.2.5 robustbase0.93-5 Biobase2.44.0 inline0.3.15 glue1.3.1
[33] rrcov1.4-7 R62.4.0 processx3.3.1 rstan2.18.2 corpcor1.6.9 ggplot23.1.1 callr3.2.0 purrr0.3.2
[41] magrittr1.5 MASS7.3-51.4 BiocGenerics0.30.0 scales1.0.0 ps1.3.0 StanHeaders2.18.1 matrixStats0.54.0 assertthat0.2.1
[49] colorspace1.4-1 lazyeval0.2.2 munsell0.5.0 crayon1.3.4

flowcore • 370 views
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The table output above doesn't appear to be formatted correctly, here is a retry:

read.FCS.out FlowJo.out
679092 403.021 679092 11249.600 679092 36962.900 679092 556.698 679092 482.432 679092 21408.400 679092 89833.200 679092 88422.000 679092 486.400 15360 1.536

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Try to set 'truncate_max_range = FALSE' to see if that helps.

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Thank You!!! Yes, it reads the .fcs correctly now.

Best regards, Suntara

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