Hi, I'm trying to use an approach I've used in the past to transform parameters in flowCore, but I get an error after running estimateLogicle that states
Error in getChannelMarker(x, channel) : can't find *593/40 [YG]
I get this message whether I specify one or several channels to transform, I've tried both indexing my 'mycolnames' list and also manually specifying a string for the parameter name(s). This is data from our BD Influx and it's running Sortware (i.e. not Spigot) for acquisision.
myfile <- list.files(pattern = "*.fcs")
myframe <- read.FCS(myfile) #read in an fcs file
mycolnames <- colnames(myframe) #get new list of parm names
ChnlsToTrans <- mycolnames[c(12,14:23)] #which parms to transform
translist <- estimateLogicle(myframe, ChnlsToTrans) #estimate logicle transform from data
Does anyone see an issue with my code? Or is this an issue with the file header? Example files are here.
----------------------
R version 3.3.3 (2017-03-06)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggcyto_1.2.3 flowWorkspace_3.20.5 ncdfFlow_2.20.2 BH_1.65.0-1 RcppArmadillo_0.8.100.1.0
[6] ggplot2_2.2.1 flowCore_1.40.6
loaded via a namespace (and not attached):
[1] pcaPP_1.9-72 Rcpp_0.12.13 bindr_0.1 DEoptimR_1.0-8 RColorBrewer_1.1-2 plyr_1.8.4 tools_3.3.3
[8] zlibbioc_1.20.0 tibble_1.3.4 gtable_0.2.0 lattice_0.20-35 pkgconfig_2.0.1 rlang_0.1.2 graph_1.52.0
[15] DBI_0.7 Rgraphviz_2.18.0 parallel_3.3.3 mvtnorm_1.0-6 hexbin_1.27.1 bindrcpp_0.2 gridExtra_2.3
[22] stringr_1.2.0 dplyr_0.7.4 cluster_2.0.6 IDPmisc_1.1.17 stats4_3.3.3 grid_3.3.3 glue_1.1.1
[29] robustbase_0.92-7 Biobase_2.34.0 data.table_1.10.4-2 R6_2.2.2 rrcov_1.4-3 XML_3.98-1.9 latticeExtra_0.6-28
[36] magrittr_1.5 corpcor_1.6.9 scales_0.5.0 matrixStats_0.52.2 BiocGenerics_0.20.0 MASS_7.3-47 assertthat_0.2.0
[43] colorspace_1.3-2 KernSmooth_2.23-15 stringi_1.1.5 flowViz_1.38.0 lazyeval_0.2.0 munsell_0.4.3
Thanks for the reply and explanation - this makes sense. And sorry for the late response, I wasn't getting notifications for some reason. From inspecting the getChannelMarker function, it seems matching uses fix = TRUE in the current version of flowCore. Which explains why I am no longer encountering this issue when working with Influx instrument data where compensated channel names always begin with "*". I don't recall how I solved this originally unfortunately. Running this below now works fine:
library(flowCore) myfile <- list.files(pattern = "*.fcs") myframe <- read.FCS(myfile) #read in an fcs file mycolnames <- colnames(myframe) #get list of parm names toKeep <- mycolnames[c(11:30)] #fluorescence and scatter parameters myframe <- myframe[,toKeep] #index to keep only these mycolnames <- colnames(myframe) #get new list of parm names toKeep <- grepl("\\*|FSC|SSC",mycolnames) #generate logical to index and keep only scatter and * containing params toKeep <- mycolnames[toKeep] #index parameter list by logical of which to keep myframe <- myframe[,toKeep] mycolnames <- colnames(myframe) #get new list of parm names ChnlsToTrans <- mycolnames #which parms to transform translist <- estimateLogicle(myframe, ChnlsToTrans) #estimate logicle transform from data