Studentizing microarray data

Microarrays let us measure relative expression levels of thousands of genes simultaneously. While there are a variety of microarray platforms (e.g., radioactively labeled cDNA on nylon membranes, Affymetrix gene chips) we will focus on spotted cDNA arrays. These involve cDNA samples labeled with fluorescent dyes, hybridized to probes spotted by a robotic arrayer onto a glass substrate. Two samples are hybridized to each array, with the two samples labeled with different dyes. The most commonly used dyes are Cy5 (red) and Cy3 (green). Scanning the array produces a greyscale intensity image for each sample; we will refer to these as the two "channels" of the array. While these two samples may both be of interest, it is often the case that there will be one sample of primary interest and the other sample will be from a "control" or "reference" substance (typically a mixture of cell lines).