[BioC] Error reading case study BeadStudio profiles with read.ilmn in limma

[Tim Kendall]

Hi,

I am trying to follow the case study ("16.3 Comparing Mammary Progenitor 
Cell Populations with Illumina BeadChips") using the example data files 
(from http://bioinf.wehi.edu.au/marray/IlluminaCaseStudy/) in the limma 
User's Guide prior to my first attempt at analysing my own data in the 
same BeadStudio profile format. The target file reads without a problem 
but the /read.ilmn/ command fails to generate the expected EListRaw 
object from the profiles; I had a brief fiddle with my own data last 
week and successfully created an EListRaw object but I think there was 
an update to limma 3.18.10 that I applied before I tried the case study 
(and I can no longer successfully read my own data after the upgrade 
either).

"/> source("http://bioconductor.org/biocLite.R")//
//Bioconductor version 2.13 (BiocInstaller 1.12.0), ?biocLite for help//
//> library("limma")//
//.....//
//> x <- read.ilmn(files="probe profile.txt",ctrlfiles="control probe 
profile.txt", other.columns="Detection")//
//Reading file probe profile.txt ... ...//
//Reading file control probe profile.txt ... ...//
//Error in `row.names<-.data.frame`(`*tmp*`, value = c(5090180L, 
6510136L,  : //
//  duplicate 'row.names' are not allowed//
//In addition: Warning message://
//non-unique values when setting 'row.names': '1110170', '2510500', 
'4010327', '4610291'/ "

For information, output of traceback attached and output from sessionInfo():

"/> sessionInfo()//
//R version 3.0.2 (2013-09-25)//
//Platform: x86_64-pc-linux-gnu (64-bit)//
//
//locale://
// [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C LC_TIME=en_GB.UTF-8 //
// [4] LC_COLLATE=en_GB.UTF-8     LC_MONETARY=en_GB.UTF-8 
LC_MESSAGES=en_GB.UTF-8 //
// [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C LC_ADDRESS=C //
//[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_GB.UTF-8 
LC_IDENTIFICATION=C //
//
//attached base packages://
//[1] stats     graphics  grDevices utils     datasets methods   base //
//
//other attached packages://
//[1] limma_3.18.10        BiocInstaller_1.12.0//
//
//loaded via a namespace (and not attached)://
//[1] tools_3.0.2/"

I haven't been able to find reports of anything similar with limma and I 
hope I'm missing something simple - apologies if that's the case.

Cheers,

Tim




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