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

[Marcus Davy]

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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