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Yannick Wurm
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220
@yannick-wurm-2314
Last seen 10.2 years ago
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
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yannick . wurm @ unil . ch
Ant Genomics, Ecology & Evolution @ Lausanne
http://www.unil.ch/dee/page28685_fr.html