Dear list, I have the following batch of 6 cel files to analyze: 3 chips hybridized with different tissue samples (with a different purified cell type in each case), and one technical replicate per tissue. For each tissue, a pool of 12 mice was used. As you can see no biological replication was performed. My question is: given that a relative large number of mice was used for pooling, and that a specific cell type is consider in each case, can I expect that the inter-individual variability be highly reduced? Right now I do not have a quantitative estimation of the expected biological(12-mice pool) vs technical variability ratio, but in the case they were of the same order, could the technical replicates be considered in order to construct typical statistics, such LPE or the LIMMA modified-t one? If bio and technical variations are of the same order, can the same distributional hypothesis used to described biological correlations be applied to technical replicates? Thanks for your help Ariel./ -- Ariel Chernomoretz, Ph.D. Centre de recherche du CHUL 2705 Blv Laurier, bloc T-367 Sainte-Foy, Qc G1V 4G2 (418)-525-4444 ext 46339