[BioC] Masking of limma objects by beadarray when loading arrayQualityMetrics

[Mark Dunning]

Hi Marcus and others,

I am now looking into this issue. I had always imagined that people with
Illumina data would pre-process using beadarray and then use limma for
downstream stuff such as linear modelling, therefore it would not be a
problem if functions such as backgroundCorrect from limma are masked. 
 
I am a bit reluctant to change the names of functions within beadarray
in case people rely on them in their scripts, so am investigating other
solutions such as that proposed by Wolfgang.

Mark

On Tue, 2009-01-06 at 10:02 +1300, Marcus Davy wrote:
> Hi,
> I just wanted to make a note of a small issue that if you use 'limma'
> combined with 'arrayQualityMetrics' there is a masking of some functions
> caused by the loaded package dependency 'beadarray'.
> 
> # Doesn't matter which way around packages are declared 'beadarray' seems to
> # be higher in the search tree
> library(limma)
> library(arrayQualityMetrics)
> 
> conflicts(where=match(c("package:limma", "package:beadarray"), search()))
> [1] "backgroundCorrect" "imageplot"         "plotMA"
> 
> find("plotMA")
> [1] "package:beadarray" "package:limma"
> 
> # Explicitly calling functions as a workaround...
> limma::plotMA(...)
> beadarray::plotMA(...)
> 
> I didn't find much in the archives about potential object masking, I think
> what was most interesting was that it didn't matter what order I loaded
> 'limma' and 'arrayQualityMetrics' (restarting R each time), the package
> 'beadarray' was always higher in the search path precedence.
> 
> 
> Marcus
> 
> 
> 
> > version
>                _   
> platform       powerpc-apple-darwin8.11.1
> arch           powerpc
> os             darwin8.11.1
> system         powerpc, darwin8.11.1
> status             
> major          2   
> minor          8.0 
> year           2008
> month          10  
> day            20  
> svn rev        46754
> language       R   
> version.string R version 2.8.0 (2008-10-20)
> > sessionInfo()
> R version 2.8.0 (2008-10-20)
> powerpc-apple-darwin8.11.1
> 
> locale:
> en_NZ.UTF-8/en_NZ.UTF-8/C/C/en_NZ.UTF-8/en_NZ.UTF-8
> 
> attached base packages:
>  [1] grid      splines   tools     stats     graphics  grDevices utils
> datasets  methods   base
> 
> other attached packages:
>  [1] arrayQualityMetrics_1.8.1 marray_1.20.0             beadarray_1.10.0
> sma_0.5.15         
>  [5] hwriter_0.93              latticeExtra_0.5-4        simpleaffy_2.18.0
> affyPLM_1.18.0     
>  [9] preprocessCore_1.4.0      gcrma_2.14.1              matchprobes_1.14.1
> RColorBrewer_1.0-2 
> [13] vsn_3.8.0                 affy_1.20.0               genefilter_1.22.0
> survival_2.34-1    
> [17] geneplotter_1.20.0        annotate_1.20.1           xtable_1.5-4
> AnnotationDbi_1.4.2
> [21] lattice_0.17-15           Biobase_2.2.1             limma_2.16.3
> 
> loaded via a namespace (and not attached):
> [1] DBI_0.2-4          KernSmooth_2.22-22 RSQLite_0.7-1      affyio_1.10.1
> > 
> 
> 
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