Using this technology, the relative expression levels in two or more sample of mRNA derived from specific tissues can be assayed for thousands of genes simultaneously. When analysing the results of array based experiments, there are a number of sources of variation that must be accounted for. These include mouse to mouse variation within a strain, sample prep variation, variations that occur between arrays and, at the lowest level, measurement error within an array. In addition, there are constraints on the design of array experiments. We are typically limited to two mRNA samples per chip.
Significant variation can occur between arrays.
Thus, the array must be treated as a blocking factor and the resulting designs will generally have an incomplete block structure. Designed experiments offer quality control, normalization and a method of analysis that takes multiple sources of variation into account. The end results are estimates of changes in gene expression levels with error bars.