[BioC] Masking of limma objects by beadarray when loading arrayQualityMetrics
Marcus Davy
mdavy at hortresearch.co.nz
Mon Jan 5 22:02:25 CET 2009
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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