[BioC] Microarray PCA/MDS/SVD

Yannick Wurm yannick.wurm at unil.ch
Tue Dec 9 13:44:48 CET 2008

Dear list,

could someone recommend a review or book on PCA/MDS/SVD/Factor  
Analysis techniques & best practices for gene expression data?

I want to visualize each of my samples (3 different conditions; 20  
timepoints - no need to visualize replication because things will  
become too messy) . But I'm frankly a bit overwhelmed by the plethora  
of options.

My doubts include:
	- when it's appropriate to use which technique
	- should I use it on my complete normalized gene expression data  
set? Or only on significant genes? Or on the covariance matrix  
between microarrays?
	- even for a simple PCA, there are an overwhelming number of  
implementations in R (ade's dudi.pca, prcomp, princomp, several in  
MASS, several in pcaMethods)

thanks :o)


          yannick . wurm @ unil . ch
Ant Genomics, Ecology & Evolution @ Lausanne

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