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

[Wolfgang Huber]

Dear Marcus

this is indeed a nasty situation, however it is solved in the
development version of arrayQualityMetrics,  which loads beadarray 
functions for its internal use via namespace, and does not attach 
beadarray to the user's search path.

http://www.bioconductor.org/packages/devel/bioc/html/arrayQualityMetrics.html

Best wishes
      Wolfgang

----------------------------------------------------
Wolfgang Huber, EMBL-EBI, http://www.ebi.ac.uk/huber

Marcus Davy ha scritto:
> 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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