On 06/03/2012 05:30 AM, Juliet [guest] wrote: > > 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? You are using an old version of R, so update to 2.15.0 and install current packages using source("http://bioconductor.org/biocLite.R") biocLite("flowCore") In your function 'col' is not defined, perhaps you meant to pass it as an argument? Try and provide a fully reproducible example. For instance even in 2.13.1 I can say library(flowCore) example(estimateLogicle) f <- function(fcs, col) { tr <- estimateLogicle(fcs, col) transform(fcs, tr) } f(samp, "FL1-H") and there is no error; what do I need to do to make your error occur on my machine? Martin > sessionInfo() R version 2.13.1 Patched (2011-09-04 r56932) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] flowCore_1.18.0 rrcov_1.3-00 pcaPP_1.8-3 mvtnorm_0.9-999 [5] robustbase_0.7-3 Biobase_2.12.1 loaded via a namespace (and not attached): [1] feature_1.2.8 graph_1.30.0 ks_1.8.8 MASS_7.3-12 stats4_2.13.1 [6] tools_2.13.1 > > -- output of 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 > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: M1-B861 Telephone: 206 667-2793