The large amount of data is a typical DNA microarray assays makes for a lot of challenges for us statisticians. I've wanted to write a simple introductory web page on this topic for a while, but have never found the time to do it well. There are a couple of recent articles on microarrays published on BioMed Central with full text available on line. The first, The Limits of Log-Ratios by Sharov et al, points out that there are mathematical constraints on the Ratio-Intensity plot and that if your data bumps up against these constraints, you may see some artefactual patterns in the plot. The second, Universal Reference RNA as a standard for microarray experiments by Novoradovskaya et al, develops a reference standard useful "for monitoring and controlling intra- and inter-experimental variation." These articles are too recent to have appeared in Medline yet. An earlier article about universal reference RNA samples is also worth mentioning.
Within the fold: assessing differential expression measures and reproducibility in microarray assays. Yang IV, Chen E, Hasseman JP, Liang W, Frank BC, Wang S, Sharov V, Saeed AI, White J, Li J, Lee NH, Yeatman TJ, Quackenbush J. Genome Biol 2002: 3(11); research0062. [Medline] [Abstract] [Full text] [PDF]
You can find an earlier version of this page on my original website.