[BioC] problems reading in a flowSet
Gabriel Yvon-Durocher [guest]
guest at bioconductor.org
Thu Sep 6 17:54:58 CEST 2012
I am having trouble reading in some FCS files into a flow core session using the flowSet function.
When I try to read the files in individually using the read.FCS command I have no problems.
Here's my code:
files.pico<-list.files('~/Documents/Flow Cytometry/Picoplankton', all.files=TRUE, full.names=TRUE)
This gives he follow error message:
Error in if (!version %in% c("FCS2.0", "FCS3.0")) stop("This does not seem to be a valid FCS2.0 or FCS3.0 file") :
argument is of length zero
However, when I load in one of the files using read.FCS it works fine, which suggests that my files which have come from BD cell quest pro are indeed valid.
p1<-read.FCS('~/Documents/Flow Cytometry/Picoplankton/01_P01.124', transform='scale', alter.names=TRUE)
Any ideas as to what might be causing the problem?
Thanks in advance.
-- output of sessionInfo():
R version 2.15.1 (2012-06-22)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)
attached base packages:
 stats graphics grDevices utils datasets methods base
other attached packages:
 flowViz_1.20.0 lattice_0.20-6 flowCore_1.22.3 rrcov_1.3-02
 pcaPP_1.9-47 mvtnorm_0.9-9992 robustbase_0.9-3 Biobase_2.16.0
loaded via a namespace (and not attached):
 feature_1.2.8 graph_1.34.0 grid_2.15.1 KernSmooth_2.23-7
 ks_1.8.8 latticeExtra_0.6-24 MASS_7.3-18 RColorBrewer_1.0-5
 stats4_2.15.1 tools_2.15.1
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