FCS files not recognized

[PaulineMaby]

Hello, I try to concatenente FCS files, but they are not recognized as FCS files even though they are classic FCS.3 files. I received this message: Error in FUN(X[[i]], ...) : 'file.fcs' is not a valid file

I tried read.FCS(in_dir,"file.fcs") I had: Error in if (!version %in% c("FCS2.0", "FCS3.0", "FCS3.1")) stop("This does not seem to be a valid FCS2.0, FCS3.0 or FCS3.1 file") : argument is of length zero

Did that ever happen to someone else?

Please find below info about my session:

session_info() Session info ----------------------------------------------------------------------------------------------- setting value
version R version 3.5.0 (2018-04-23) system x86_64, darwin15.6.0
ui RStudio (1.1.453)
language (EN)
collate C
tz Europe/Paris
date 2018-09-22

Packages --------------------------------------------------------------------------------------------------- package version date source
base 3.5.0 2018-04-24 local
Biobase 2.40.0 2018-05-01 Bioconductor
BiocGenerics 0.26.0 2018-05-01 Bioconductor
cluster 2.0.7-1 2018-04-13 CRAN (R 3.5.0)
compiler 3.5.0 2018-04-24 local
corpcor 1.6.9 2017-04-01 CRAN (R 3.5.0)
datasets 3.5.0 2018-04-24 local
DEoptimR 1.0-8 2016-11-19 CRAN (R 3.5.0)
devtools 1.13.6 2018-06-27 CRAN (R 3.5.0)
digest 0.6.17 2018-09-12 CRAN (R 3.5.0)
flowCore 1.47.9 2018-09-22 Github (RGLab/flowCore@2827a9b)
graph 1.58.0 2018-05-01 Bioconductor
graphics 3.5.0 2018-04-24 local
grDevices 3.5.0 2018-04-24 local
grid 3.5.0 2018-04-24 local
lattice 0.20-35 2017-03-25 CRAN (R 3.5.0)
MASS 7.3-50 2018-04-30 CRAN (R 3.5.0)
matrixStats 0.54.0 2018-07-23 cran (@0.54.0)
memoise 1.1.0 2017-04-21 CRAN (R 3.5.0)
methods 3.5.0 2018-04-24 local
mvtnorm 1.0-8 2018-05-31 CRAN (R 3.5.0)
parallel 3.5.0 2018-04-24 local
pcaPP 1.9-73 2018-01-14 CRAN (R 3.5.0)
premessa 0.2.3 2018-09-22 Github (ParkerICI/premessa@c47abca) Rcpp 0.12.18 2018-07-23 cran (@0.12.18)
robustbase 0.93-0 2018-04-24 CRAN (R 3.5.0)
rrcov 1.4-4 2018-05-24 CRAN (R 3.5.0)
stats 3.5.0 2018-04-24 local
stats4 3.5.0 2018-04-24 local
tools 3.5.0 2018-04-24 local
utils * 3.5.0 2018-04-24 local
withr 2.1.2 2018-03-15 CRAN (R 3.5.0)

[pfgherardini]

Hi

It looks like this is not specific to premessa as even flowCore is having trouble with that file. If you share it with me on Box / Dropbox i can take a look

Thanks

[PaulineMaby]

Thank you very much for your interest. I solved the problème few months ago. I just had to update one if my R package. It is really nice if you to propose your help anyway. Best regards Pauline

Le mar. 29 janv. 2019 19:49, Pier Federico Gherardini < notifications@github.com> a écrit :

Hi

It looks like this is not specific to premessa as even flowCore is having trouble with that file. If you share it with me on Box / Dropbox i can take a look

Thanks

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