I'm having a hard time understanding what I need to to prepare for FlowTrans input files. Please take a look at the following command lines (below). The example input file has no problem taking the file, I'm not sure what's missing with FCS3? I used a regular fcs3 files that I imported from flowJo. Thank you!

> fcstrans <- flowTrans(fcs,"mclMultivBiexp",colnames(fcs)[0:14], n2f=FALSE, parameters.only=FALSE)

> print(colnames(fcs)[0:14])
 [1] "FSC-A"           "FSC-H"           "FSC-W"           "SSC-A"           "SSC-H"         
 [6] "SSC-W"           "FITC-A"          "PE-A"            "APC-A"           "PerCP-Cy5-5-A" 
[11] "PE-Cy7-A"        "Violet 530_30-A" "Time"            "Event #"    

> print(colnames(GvHD[[1]])[1:2])  ## testing the example file

[1] "FSC-H" "SSC-H"

> contour(fcs[,0:3], main="Untransformed FSC vs SSC") ## got a contour plot

> contour(fcstrans$fcstrans[,0:3], main="Transformed FSC vs SSC")

Error in seq.default(0, 1, length.out = ncol(z)) :
  argument 'length.out' must be of length 1
> contour(fcstrans$fcstrans[,1:4], main="Transformed FSC vs SSC")

Error in seq.default(0, 1, length.out = ncol(z)) :
  argument 'length.out' must be of length 1

> contour(fcstrans[,0:3], main="Transformed FSC vs SSC")

Error in contour(fcstrans[, 0:3], main = "Transformed FSC vs SSC") :
  error in evaluating the argument 'x' in selecting a method for function 'contour': Error in fcstrans[, 0:3] : incorrect number of dimensions