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 > The contents of this e-mail are confidential and may be ...{{dropped:8}}

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/arrayQualityMetri cs.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 > > > The contents of this e-mail are confidential and may be ...{{dropped:8}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

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 > > > > > The contents of this e-mail are confidential and may be ...{{dropped:8}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor