4.2 years ago by
Your goal is an unconventional one for the microarray context, especially a two-color microarray. In other words, an expression value really doesn't mean anything by itself, but is only useful when compared to the expression of the same gene in a different sample. In addition, standard errors of technical replicates only tell you how reproducible the technology is, not how variable the gene expression is, across your sample (and presumably across the population of interest).
Ideally you would analyze this as a two-color array, in which case you would compute (and use) the log ratios that are inherent to this sort of design. Do note that starting on p. 38 (and again on p 54) of the limma User's Guide, there are examples that directly relate to what you are doing. But this will not result in individual gene expression values for each gene, but instead will give you log ratios.
If you are truly interested in expression estimates for each gene, then you likely have to do a separate analysis of two-color data, which is covered in the limma User's Guide starting on p. 58.