We present a detailed method to analyze
DNA copy number data generated on
cDNA microarrays. A web interface is made available for those steps in the workflow that are not typically used in gene expression analysis so that these steps can be carried out online. The end result of the analysis is a list of
p -values for the presence of genomic gains or losses for each sample individually or an average
p -value, which we show is useful to identify recurrent genomic imbalances.
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