Project VI: Normalization and standardization in microarray experiments

One problematic area in the analysis of microarray data is that of array normalization: typically there is considerable systematic, but not expression related variation within an array and variation across replicate arrays. Before a set of differentially-expressed genes can be identified, the array must be normalized so that spurious results are not reported. The sources of this unwanted variation between arrays are often due to slight differences in the construction of the arrays, or different spotting machinery, or imperfect imaging results. This phenomenon arises in cDNA and oligonucleotide arrays.

Many methods of normalization/standardization of microarray data have been proposed, and this project will investigate some of them. Methods of within-array adjustment (correcting for nonlinear relationships between total signal ad observed match/mismatch difference) and between-array standardization (baseline methods, quantile normalization) will be studied.

A large test data set, concerning the transcriptome derived from human chromosomes 21 and 22 will be investigated in some detail.