[BioC] estimateLogicle from flowCore produces \"Error in eval(expr, envir, enclos) : object \'tr\' not found\" error

[Juliet [guest]]

I am trying to analyse some flow cytometry data using flowCore.

The problem I have is that I am using the estimateLogicle function and this is giving me an error with one of my files when I run it from within a function:

gating <- function(file, name, results.dir){
   fcs <- read.FCS(file)
   tr <- estimateLogicle(fcs, col)
   fcs <- transform(fcs, tr)
}

For one of my files, I get the following error message:

"Error in eval(expr, envir, enclos) : object 'tr' not found"

I think that this comes from the transform function when you are trying to the apply the results from estimateLogicle...

The weird thing is that when I actually run these arguments by hand then it works without giving me an error... but when I run it from within the function it gives me an error.

Do you know what the problem is?

 -- output of sessionInfo(): 

> sessionInfo()
R version 2.13.1 (2011-07-08)
Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)

locale:
[1] C/en_US.UTF-8/C/C/C/C

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

other attached packages:
[1] flowCore_1.18.0  rrcov_1.3-01     pcaPP_1.9-43     mvtnorm_0.9-9991 robustbase_0.7-6 Biobase_2.12.2  

loaded via a namespace (and not attached):
[1] MASS_7.3-14   feature_1.2.7 graph_1.30.0  ks_1.8.2      stats4_2.13.1 tools_2.13.1 

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