[BioC] Re: Manova nuances
Liaw, Andy
andy_liaw at merck.com
Fri Nov 21 14:12:49 MET 2003
> From: Stephen P. Baker [mailto:stephen.baker at umassmed.edu]
>
> Principle component analyses should reduce your data array to
^^^^^^^^^
Principal
> as many independent components as you have samples, and for
> each sample get a score for each dimension. These will have
> the same total information as the original data. These can
> then be analysed separately with univariate anova but since
> these are "orthogonal" analyses, multiple comparisons
> adjustments would not be needed.
The analysis you described is quite different than MANOVA, so
the conclusion/interpretation would be quite different, too.
MANOVA treats the data as coming from multivariate normal
distribution, and tests whether all groups have the same
mean vector. What you described is n (number of samples) ANOVA
analyses that gives n p-values.
Cheers,
Andy
Andy Liaw, PhD
Biometrics Research PO Box 2000, RY33-300
Merck Research Labs Rahway, NJ 07065
mailto:andy_liaw at merck.com 732-594-0820
> -.- -.. .---- .--. ..-.
> Stephen P. Baker, MScPH , PhD(ABD) (508) 856-2625
> Senior Biostatistician
> (775) 254-4885 fax
> Academic Computing Services
> Lecturer in Biostatistics , Graduate School of Biomedical
> Sciences University of Massachusetts Medical School
> 55 Lake Avenue North
> stephen.baker at umassmed.edu
> Worcester, MA 01655 USA
> --------------------------------------------------------------
> --------------
> ----
> Date: Fri, 21 Nov 2003 00:18:54 -0500
> From: "Michael Benjamin" <msb1129 at bellsouth.net>
> Subject: [BioC] Manova nuances
> To: <bioconductor at stat.math.ethz.ch>
> Message-ID: <003401c3afee$f7eff000$7a05fea9 at amd>
> Content-Type: text/plain; charset="US-ASCII"
>
>
> Anybody here using manova? It's powerful and pretty fast,
> but I'm finding that you can't have more variables than
> samples (limits its applicability to microarray research).
> Is there any way around this? Assume
>
> dim(eset)
>
> 1200 35
>
> transeset<-t(eset)
> fit<-manova(transeset ~ categories)
> summary(fit)
>
> There is probably a complicated mathematical truth that
> underlies this limitation--if anybody can shed some light,
> that would be great.
>
> Also, if anyone knows of a quick, free multivariate tool that
> summarizes all the tests into a single test statistic, that
> would be much appreciated.
>
> Regards,
> Michael Benjamin, MD
> Emory University
> Winship Cancer Institute
>
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