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*

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