Dear Bioconductors arrayQualityMetrics_3.2.3 is now available from the release branch. To update your existing version, what you need to do is run source("http://bioconductor.org/biocLite.R") update.packages(repos=biocinstallRepos(), ask=FALSE, checkBuilt=TRUE) in R-2.12. It fixes two issues that were discussed on this list recently: 1. Incompatibility between the R package SVGAnnotation_0.7-0 and the system library libcairo 1.10 (Duncan has recently released SVGAnnotation_0.7-2, on which arrayQualityMetrics now depends). 2. Overzealous error throwing for some Affymetrix genechip datasets that have no MMs, as was recently noted by Tim (https://stat.ethz.ch/pipermail/bioconductor/2010-November/036372.html ). * * * One thing to note: SVGAnnotation does not work with very old versions of libcairo. If you run into this, you'll either need to update your libcairo, or also use an old version of arrayQualityMetrics. Btw, more interactivity enhancements are under way for arrayQualityMetrics in the current devel branch - but this is not yet fit for production use and will need a few more weeks. Best wishes Wolfgang Il Oct/21/10 10:40 AM, Wolfgang Huber ha scritto: > > This will manifest itself by seeing the error message > > Error in aqm.highlight(doc, annotationInfo = annotationInfo) : > 'length(annotationInfo$annotation)' must be equal to 'length(series)', > the number of objects in the plot. > > The reason appears to be a misfit between R's SVG-device and the package > SVGAnnotation that seems to have entered just a few days before > R-2.12.0's release. I am working on a solution and will announce it here. > > As a workaround until then, please use > http://www.bioconductor.org/packages/2.6/bioc/html/arrayQualityMetri cs.html > (For R-2.12 users: first install the package as usual with "biocLite", > then manually download the version above and install it over that.) > > Sorry for the trouble. > > Best wishes > Wolfgang Huber > EMBL > http://www.embl.de/research/units/genome_biology/huber > > _______________________________________________ > 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