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

[Gordon K Smyth]

Dear Tim,

My fault.  I introduced an "improvement" to read.ilmn() on 31 January, but 
forgot that the Illumina probe IDs might not all be unique and so might 
not be allowable as rownames for the gene annotation data.frame.  I have 
fixed it today.

The limma change-log tells the story:

  5 February 2014: limma 3.18.11

- The change to read.ilmn() in 3.18.10 caused an error when the
   Illumina probe IDs were not all unique.  The probe IDs are now used
   as row.names for the annotation data.frame only when they are
   unique.

31 January 2014: limma 3.18.10

- read.ilmn() now sets the same probe IDs as rownames for both the
   expression matrix E and the annotation data.frame genes.

Best wihes
Gordon



------------- original message -------------
Tim Kendall Tim.Kendall at ed.ac.uk
Tue Feb 4 16:50:13 CET 2014

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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