Article,
Comparison of algorithms for the analysis of Affymterix microarray data as evaluated by co"=expression of genes in known operons
Nucleic Acids Research, 34 (2): e8 (2006)
Abstract
Oligonucleotide microarrays are an informative tool to elucidate gene
regulatory networks. In order for gene expression levels to be comparable
across microarrays, normalization procedures have to be invoked.
A large number of methods have been described to correct for systematic
biases in microarray experiments. The performance of these methods
has been tested only to a limited extend. Here, we evaluate two different
types of microarray analyses: (i) the same gene in replicate samples
and (ii) different, but co-expressed genes in the same sample. The
reliability of the latter analysis needs to be determined for the
analysis of regulatory networks and our report is the first attempt
to evaluate for the accuracy of different microarray normalization
methods in this respect. Consistent with previous results we observed
a large effect of the normalization method on the outcome of the
expression analyses. Our analyses indicate that different normalization
methods should be performed depending on whether a study is aiming
to detect differential gene expression between independent samples
or whether co-expressed genes should be identified. We make recommendations
about the most appropriate method to use.
