Microarray Analysis and Processing

In order to determine whether measured mRNA levels or other global data are consistent with a particular model of a cellular process, we need to have some notion of how much measurement error and biological variation can influence the measurements. Accordingly, we have developed refined statistical procedures, based on maximum-likelihood estimation, to determine which changes observed with a DNA microarray are significant and which are likely due to error [Ideker et al. Journal of Computational Biology 7: 805-817 2000]. These methods are available for download (Windows, Linux, and SunOS platforms) through the public-domain software package VERA and SAM [link to software]. More recently, these methods have been corrected for the effects of gene-specific dye bias [Kelley et al. Bioinformatics Jul 10 2007].