[BioC] problems reading in a flowSet

Gabriel Yvon-Durocher [guest] guest at bioconductor.org
Thu Sep 6 17:54:58 CEST 2012

Dear all,

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)

[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

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

other attached packages:
[1] flowViz_1.20.0     lattice_0.20-6     flowCore_1.22.3    rrcov_1.3-02      
[5] pcaPP_1.9-47       mvtnorm_0.9-9992   robustbase_0.9-3   Biobase_2.16.0    
[9] BiocGenerics_0.2.0

loaded via a namespace (and not attached):
 [1] feature_1.2.8       graph_1.34.0        grid_2.15.1         KernSmooth_2.23-7  
 [5] ks_1.8.8            latticeExtra_0.6-24 MASS_7.3-18         RColorBrewer_1.0-5 
 [9] stats4_2.15.1       tools_2.15.1 

Sent via the guest posting facility at bioconductor.org.

More information about the Bioconductor mailing list