After running, getMonograph() I get the warning: Warning message: package ?arrayMagic? is not available I see this package is not longer available with Bioconductor 2.2 Software Packages. I don't know if this is critical or not?

The arrayMagic package last appeared in the Bioconductor 2.1 release and can still be downloaded for use with R 2.6. Bioconductor employs a creative destructive process where software is retired (made defunct) at the end of its software life cycle and that happened with arrayMagic during the creation of Bioconductor 2.2. When a package is made defunct there typically is an alternative package out there that addresses the issues handled by the old one. Are there particular applications that you were looking to use arrayMagic for? Patrick A.I. McLeod wrote: > After running, > getMonograph() > > I get the warning: > > Warning message: > package ?arrayMagic? is not available > > I see this package is not longer available with Bioconductor 2.2 Software > Packages. > > I don't know if this is critical or not? > > _______________________________________________ > 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 Ian, We will need to fix that, and I suspect that it and other changes in packages since that book was written will make some of the code less useful. We are now planning a new edition, but probably that is year or so off. In the meantime, please feel free to ask direct questions, and I will see how much of the book we can renovate to use the more recent approaches. However, there are two other options you might consider: from an applications point of view, the Bioconductor Case Studies book, is more up to date and provides a reasonable coverage some details are here: http://www.bioconductor.org/pub/biocases/ and from a programming perspective: http://www.bioconductor.org/pub/RBioinf/ provides a deeper look at the tools that underly most of the software packages, best wishes Robert A.I. McLeod wrote: > After running, > getMonograph() > > I get the warning: > > Warning message: > package ?arrayMagic? is not available > > I see this package is not longer available with Bioconductor 2.2 Software > Packages. > > I don't know if this is critical or not? > > _______________________________________________ > 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 > -- Robert Gentleman, PhD Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 PO Box 19024 Seattle, Washington 98109-1024 206-667-7700 rgentlem at fhcrc.org