[BioC] Distance function and gene expression standardization for clustering

[Serge Eifes]

Dear all,

We have performed a time-scale experiment including different time-points
(0h, 2h, 6h, .). Treated and untreated cells were compared by competitive
hybridizations on every time-point using dual-channel microarrays. 

Now we want to detect groups of genes affected by the same TFs using a gene
clustering approach based on the set of differentially expressed genes.

 Is it generally appropriate to perform gene expression standardization
(e.g. by rescaling and recentering) on logged fold changes using such an
experimental design independently of the distance function used (e.g.
euclidean distance, pearson correlation, cosine correlation, .)? What is the
impact of such a standardization approach on the clustering results?

I would appreciate any comments or suggestions.

Regards,
Serge Eifes




Serge Eifes
Laboratoire de Biologie Moleculaire et Cellulaire du Cancer (LBMCC)
Hopital Kirchberg 
9,rue Edward steichen 
L-2540 LUXEMBOURG