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Last seen 10.5 years ago
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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