[BioC] pca analysis/plotting in 3D

[aedin culhane]

Hi,
PCA is also quite simple using ade4.

install.package("ade4")
library(ade4)
 
data(rhone)
dd1 <- dudi.pca(rhone$tab, nf = 4, scann = FALSE)
scatter(dd1, sub = "Principal component analysis")

For more examples: 

example(dudi.pca) # principal component analysis
example(dudi.coa) # Correspondence analysis eg: fellenberg et al., 2001


Aedin Culhane


On Wed, 2003-11-26 at 07:43, Natalie Thorne wrote:
> PCA analysis is simple enough using prcomp function from the mva R
> library.  The help is quite good so you should be able to figure it out
> from there.
> 
> For 3D plots try the R library package xgobi...I've used it before and its
> quite good.
> 
> Natalie
> 
>      *   *    Natalie Thorne, Phd Student.
>    *     *
>    *   *      Genetics and Bioinformatics Division,
>      *	      The Walter And Eliza Hall Institute
>    *   *      Of Medical Research (WEHI).
>    *     *    PO Royal Melbourne Hospital, 3050
>      *   *    PH:    +61 3 9345 2631
>        *      Fax:   +61 3 9347 0852
>      *   *    URL http://bioinf.wehi.edu.au
>    *     *
>    *   *      Mathematics and Statistics Department,
>      *        The University of Melbourne
>    *   *      Fax:   +61 3 9344 4599
>    *     *
>      *   *
>        *      CRC for discovery of genes for common
>      *   *    human diseases.
>    *     *
>    *   *      Email : thorne at wehi.edu.au
> 
> On Wed, 26 Nov 2003, Anthony Bosco wrote:
> 
> > Hi.
> >
> > I am interested in doing pca analysis on affymetrix data and ploting
> > 3 components (in 3-D).
> >
> > Does anyone know how to do this?
> >
> >
> > Regards
> >
> >
> > Anthony
> >
> > --
> > ______________________________________________
> >
> > Anthony Bosco - Cell Biology Research Assistant
> >
> > Institute for Child Health Research
> > (Company Limited by Guarantee ACN 009 278 755)
> > Subiaco, Western Australia, 6008
> >
> > Ph 61 8 9489  , Fax 61 8 9489 7700
> > email anthonyb at ichr.uwa.edu.au
> >
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-- 
Aedin Culhane
Conway Institute
University College Dublin
Belfied, Dublin 4
Ireland

Phone: +353 (0)1 7166834
Fax:   +353 (0)1 7166701
Email:	Aedin.Culhane at ucd.ie