Hi Drs. Carey and Altman, I think MAANOVA is probably closer to what I want, although it just dawned on me that GGtools may be closer still. I have most every piece of data I could possibly ask for on ~200 patients, now I'm trying to determine possible common mechanisms for disease progression that can be identified across the various types of driver aberrations. I copped out and fitted univariate models with nested variance terms to each locus, just for now. Something like a reduced-representation MANOVA is closer to what I really want, though. However, now that you and Dr. Altman bring up block structure across arrays, have others applied TANOVA to microarray data with varying followup time points? When I tried it on a dataset, I ran into this problem, and couldn't find a satisfactory solution. It's not relevant to my current project but it is of significant interest for another one. Thank you for your replies and time, --tim On Wed, Mar 9, 2011 at 5:06 PM, Vincent Carey <stvjc@channing.harvard.edu>wrote: > Briefly, you should read the help for duplicateCorrelation and the > lmFit man pages to see what limma is capable of when there is a block > structure across arrays. > > On Wed, Mar 9, 2011 at 6:03 PM, Tim Triche, Jr. <tim.triche@gmail.com> > wrote: > > I must be dense, because I can't seem to figure out how a person would > use > > limma to fit a linear mixed model. Is this because doing so would > involve > > trying to do a Cholesky decomposition on a huge-by-huge matrix, and > likely > > lead to flames shooting out the sides of my computer? > > > > Seems like a relatively straightforward thing to do but most challenging > > problems appear that way. Should I stick to trying lme4 for this > purpose? > > It seems a shame not to regularize with eBayes. > > > > -- > > If people do not believe that mathematics is simple, it is only because > they > > do not realize how complicated life is. > > John von Neumann< > http://www-groups.dcs.st- and.ac.uk/~history/Biographies/Von_Neumann.html> > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > -- The good Christian should beware of mathematicians, and all those who make empty prophecies. The danger already exists that the mathematicians have made a covenant with the devil to darken the spirit and to confine man in the bonds of Hell. Saint Augustine the Blessed<http: www.math.osu.edu="" ~easwaran="" augustine.html=""> , *De Genesi ad Litteram* [[alternative HTML version deleted]]