Just a few links to helpful sites (Links in green).
Free Statistical Software
More Free Software
PowerAnalysis, who knew power analyses could be so much fun.
More links found here
Pathway Analysis: The two that works the best
GeneTools: Annotation Database
Important Papers on Microarray Analyses
Statistical design and the analysis of gene expression microarray data
Using ANOVA to analyze microarray data
Fundamentals of experimental design for cDNA microarrays.
The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies.
Assessing gene significance from cDNA microarray expression data via mixed models.
Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation.
Design issues for cDNA microarray experiments.