Hello, I am having a merging issue with cytofkit version 1.2.4 run on R 3.2.4.

I am trying to run an analysis on couples of .fcs files. Unfortunately I cannot post the files as they are confidential. 

Here's the code and the error message: 

files <- list.files(path="C:/Users/data", pattern='.fcs$', full=TRUE)
paraFile <- list.files(path="C:/Users/data", pattern='.txt$', full=TRUE)
parameters <- as.character(read.table(paraFile, sep = "\t", header = TRUE)[, 1])
ID_047<-files[16:17]
merged_ID047<-cytof_exprsMerge(ID_047, markers=parameters,fixedNum = 500)

Error in y@f(x[, y@input]) : 
  Logicle Exception: DidNotConverge: scale() didn't converge 

I can't figure out what is wrong. I have tried with the GUI with the same results. Can anybody help?

For completeness, here's the output of traceback()

10: .Call("logicle_transform", as.double(x), as.double(t), as.double(w), 
        as.double(m), as.double(a))
9: y@f(x[, y@input])
8: translist %on% `_data`
7: translist %on% `_data`
6: .local(`_data`, ...)
5: flowCore::transform(fcs, trans)
4: flowCore::transform(fcs, trans)
3: (function (fcsFile, comp = FALSE, verbose = FALSE, markers = NULL, 
       transformMethod = "auto_lgcl", scaleTo = NULL, w = 0.1, t = 4000, 
       m = 4.5, a = 0, q = 0.05) 
   {
       name <- sub(".fcs", "", basename(fcsFile))
       if (verbose) {
           fcs <- read.FCS(fcsFile)
       }
       else {
           fcs <- suppressWarnings(read.FCS(fcsFile))
       }
       if (comp == TRUE) {
           if (comp && !is.null(fcs@description$SPILL)) {
               fcs <- applyComp(fcs, "SPILL")
           }
           else if (comp && !is.null(fcs@description$SPILLOVER)) {
               fcs <- applyComp(fcs, "SPILLOVER")
           }
           else if (comp && !is.null(fcs@description$COMP)) {
               fcs <- applyComp(fcs, "COMP")
           }
       }
       pd <- fcs@parameters@data
       if (!(is.null(markers))) {
           right_marker <- markers %in% pd$desc || markers %in% 
               pd$name
           if (!(right_marker)) {
               stop("\n Selected marker(s) is not in the input fcs files \n please check your selected markers! \n")
           }
           else {
               desc_id <- match(markers, pd$desc)
               name_id <- match(markers, pd$name)
               mids <- c(desc_id, name_id)
               marker_id <- unique(mids[!is.na(mids)])
           }
       }
       else {
           marker_id <- 1:ncol(fcs@exprs)
       }
       if (transformMethod == "auto_lgcl") {
           trans <- auto_lgcl(fcs, channels = colnames(fcs@exprs)[marker_id])
           transformed <- flowCore::transform(fcs, trans)
           exprs <- transformed@exprs[, marker_id]
       }
       else if (transformMethod == "fixed_lgcl") {
           trans <- flowCore::logicleTransform(w = w, t = t, m = m, 
               a = a)
           exprs <- apply(fcs@exprs[, marker_id], 2, trans)
       }
       else if (transformMethod == "arcsin") {
           trans <- flowCore::arcsinhTransform(a = 1, b = 1, c = 1)
           exprs <- apply(fcs@exprs[, marker_id], 2, trans)
       }
       else if (transformMethod == "biexp") {
           trans <- flowCore::biexponentialTransform(a = 0.5, b = 1, 
               c = 0.5, d = 1, f = 0, w = 0)
           exprs <- apply(fcs@exprs[, marker_id], 2, trans)
       }
       else {
           stop("transformMethod [", transformMethod, "] doesn't exist for cytofkit!")
       }
       if (!is.null(scaleTo)) {
           exprs <- apply(exprs, 2, function(x) scaleData(x, scaleTo))
       }
       col_names <- paste0(pd$name, "<", pd$desc, ">")
       colnames(exprs) <- col_names[marker_id]
       row.names(exprs) <- paste(name, 1:nrow(exprs), sep = "_")
       return(exprs)
   })(dots[[1L]][[1L]], comp = FALSE, verbose = FALSE, markers = c("162Dy_CD45RA", 
   "164Dy_CD20", "166Er_CD33", "167Er_CD28", "168Er_CD24", "170Er_CD161", 
   "151Eu_CD38", "153Eu_CD11b", "155Gd_CCR6", "156Gd_CD94", "157Gd_CD86", 
   "158Gd_CXCR5", "160Gd_CCR7", "165Ho_CD127", "113In_CD57", "175Lu_HLADR", 
   "142Nd_CD19", "143Nd_CD4", "144Nd_CD8", "146Nd_IgD", "148Nd_CD11c", 
   "150Nd_CD3", "147Sm_CD85j", "149Sm_CD16", "152Sm_CD27", "154Sm_CD14", 
   "159Tb_CXCR3", "169Tm_ICOS", "171Yb_TCRgd", "172Yb_PD-1", "173Yb_CD123", 
   "174Yb_CD56", "176Yb_CD25"), transformMethod = "auto_lgcl", scaleTo = NULL, 
       w = 0.1, t = 4000, m = 4.5, a = 0, q = 0.05)
2: mapply(cytof_exprsExtract, fcsFiles, MoreArgs = list(comp = comp, 
       verbose = verbose, markers = markers, transformMethod = transformMethod, 
       scaleTo = scaleTo, w = w, t = t, m = m, a = a, q = q), SIMPLIFY = FALSE)
1: cytof_exprsMerge(ID_047, markers = parameters, fixedNum = 500)

And the output of sessionInfo()

R version 3.2.4 Revised (2016-03-16 r70336)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

locale:
[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252   
[3] LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                           
[5] LC_TIME=English_United Kingdom.1252    

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

other attached packages:
[1] cytofkit_1.2.4 plyr_1.8.3     ggplot2_2.1.0 

loaded via a namespace (and not attached):
 [1] gtools_3.5.0        reshape2_1.4.1      splines_3.2.4       lattice_0.20-33    
 [5] tcltk_3.2.4         pcaPP_1.9-60        colorspace_1.2-6    htmltools_0.3.5    
 [9] stats4_3.2.4        mgcv_1.8-12         flowCore_1.36.9     e1071_1.6-7        
[13] BiocGenerics_0.16.1 matrixStats_0.50.1  foreach_1.4.3       robustbase_0.92-5  
[17] stringr_1.0.0       munsell_0.4.3       pdist_1.2           gtable_0.2.0       
[21] caTools_1.17.1      mvtnorm_1.0-5       codetools_0.2-14    VGAM_1.0-1         
[25] Biobase_2.30.0      permute_0.9-0       doParallel_1.0.10   httpuv_1.3.3       
[29] parallel_3.2.4      class_7.3-14        DEoptimR_1.0-4      Rcpp_0.12.4        
[33] KernSmooth_2.23-15  xtable_1.8-2        corpcor_1.6.8       scales_0.4.0       
[37] gdata_2.17.0        vegan_2.3-5         graph_1.48.0        mime_0.4           
[41] gplots_3.0.1        RANN_2.5            digest_0.6.9        stringi_1.0-1      
[45] Rtsne_0.10          shiny_0.13.2        grid_3.2.4          tools_3.2.4        
[49] bitops_1.0-6        magrittr_1.5        cluster_2.0.3       rrcov_1.3-11       
[53] Matrix_1.2-4        MASS_7.3-45         reshape_0.8.5       iterators_1.0.8    
[57] R6_2.1.2            igraph_1.0.1        nlme_3.1-125  

Thanks

Margherita