ABSTRACT

In many cases, the purpose of the microarray experiment is to compare the gene expression levels between two different phenotypes.1 In most cases, one sample is considered the reference or control and the other one is considered the experiment. Obvious examples include comparing healthy versus disease, treated versus untreated, drug A versus drug B, before and after treatment, etc. Sample comparison may be done using different arrays (e.g., oligonucleotide arrays) or multiple channels on the same array (e.g., cDNA or Illumina arrays). In all such comparative studies, a very important problem is to

being compared.