[BioC] xy-plot of fcs fails: undefined column selected
Jiang, Mike
wjiang2 at scharp.org
Fri Jun 13 19:43:10 CEST 2014
Try back tic instead of quote marks ,I.e.
`SSC-A` ~ `FSC-A`
Mike
________________________________________
From: Tobias Timmel [guest] [guest at bioconductor.org]
Sent: Friday, June 13, 2014 6:59 AM
To: bioconductor at r-project.org; tobias.timmel at charite.de
Cc: Jiang, Mike
Subject: xy-plot of fcs fails: undefined column selected
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:
---8<---
library(flowCore)
library(flowViz)
sample <- read.FCS("sample.fcs", transformation=FALSE)
xyplot("SSC-A" ~ "FSC-A", data=sample)
---8<---
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,
Tobias
--
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)
locale:
[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
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=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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