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      

Hi,

The code of the getChannelMarker function tries to find an exact match using of the .flowParamMatch function. By default the matching is not in fix mode (fix = FALSE) but considers the query as a regular expression. This leads to a call to the grepl() function. As the mentioned channel contains special characters, the channel is not taken asis. The "[YD]" is searched as a Y or D character. Therefore, the getChannelMarker fails. IMHO, the fix option should be set to TRUE in the getChannelMarker. While the estimateLogicle function allow extra parameters ..., those parameters are transferred to the logicle transformation, not to getChannelMarker.

Let's wait for Mike's opinion.

HTH