statmod does not get installed along with limma. Even if I install statmod manually, it does not load when limma is loaded (although it does when it is needed). This problem has persisted for several generations of limma. --Naomi

Hi Naomi, Please start a new thread, rather than responding to an existing thread and simply changing the subject line. For those of us using a thread-aware email client, this appears to be part of the '2 way anova in Bioconductor' thread. On 6/29/2011 12:01 PM, Naomi Altman wrote: > statmod does not get installed along with limma. Even if I install > statmod manually, it does not load when limma is loaded (although it > does when it is needed). This problem has persisted for several > generations of limma. This isn't a problem, it is a feature. The statmod package is listed as a suggested package, rather than a dependency, so it won't be installed by default, nor will it be loaded by default. Suggested packages are those that are not critical to the functionality of a package, but that can extend functionality in certain circumstances. Since statmod is only used in cases where end users choose to fit mixed models (likely a fairly rare event, and done so by more sophisticated users), listing statmod in suggests reduces downloads and loading of something not likely to be useful for the average limma user. Best, Jim > > --Naomi > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician Douglas Lab University of Michigan Department of Human Genetics 5912 Buhl 1241 E. Catherine St. Ann Arbor MI 48109-5618 734-615-7826 ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues