Hello all, I have experiment where a large fraction of genes are expected to be differentially expressed. That why I would like to normalize the data using spike control spots (I really would like to do within arrays normalization just subtract over the whole array ( or witnin i-th block) mean of log- ratio of spike control from log-ratio for each gene). I use Limma. My question is: does limma have options for such normalization? If it does not that package I should use? Sincerely, Natalia.