[BioC] xy-plot of fcs fails: undefined column selected

Tobias Timmel [guest] guest at bioconductor.org
Fri Jun 13 15:59:35 CEST 2014

Dear Bioconductor community,

I've just started to process my flow cytometry data with the R Bioconductor packages. After reading a fcs file into a flowFrame I tried to make an xy-plot: 

sample <- read.FCS("sample.fcs", transformation=FALSE)
xyplot("SSC-A" ~ "FSC-A", data=sample)

Plotting fails and I get the following error: 

Error in `[.data.frame`(ranges, , channel.x.name) : 
  undefined columns selected

When playing around with the provided example data (GvHD), however, xy-plots are fine. 

Any idea how to solve this problem? Is it a matter of my fcs file? It's a standard export from an FACSCanto2 machine using FacsDiva software.

Best regards,
 Dr. Tobias Timmel
 Muscle Research Unit
 Experimental and Clinical Research Center (ECRC)
 Charité Universitätsmedizin Berlin and Max Delbrück Center Berlin

 -- output of sessionInfo(): 

R version 3.1.0 (2014-04-10)
Platform: x86_64-pc-linux-gnu (64-bit)

 [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C               LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8     LC_MONETARY=de_DE.UTF-8   
 [6] LC_MESSAGES=de_DE.UTF-8    LC_PAPER=de_DE.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            

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

other attached packages:
[1] flowViz_1.28.22 lattice_0.20-29 flowCore_1.30.7

loaded via a namespace (and not attached):
 [1] Biobase_2.24.0      BiocGenerics_0.10.0 corpcor_1.6.6       DEoptimR_1.0-1      graph_1.42.0        grid_3.1.0          hexbin_1.26.3      
 [8] IDPmisc_1.1.17      KernSmooth_2.23-12  latticeExtra_0.6-26 MASS_7.3-33         mvtnorm_0.9-9995    parallel_3.1.0      pcaPP_1.9-49       
[15] RColorBrewer_1.0-5  robustbase_0.91-1   rrcov_1.3-4         stats4_3.1.0        tools_3.1.0   

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