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) Charit?? Universit??tsmedizin Berlin and Max Delbr??ck 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 -- Sent via the guest posting facility at bioconductor.org.

Try back tic instead of quote marks ,I.e. `SSC-A` ~ `FSC-A` Mike ________________________________________ From: Tobias Timmel [guest] [guest@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) Charit? Universit?tsmedizin Berlin and Max Delbr?ck 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 -- Sent via the guest posting facility at bioconductor.org.