Hi BioC users I am working with affymetrix exon array data of 40 samples with 8 different groups and 5 replicates of each. Two different strains are used in this study. Cells were cultured for either 3 days or 7 days. At 3 days the cells are still proliferating and are not considered mature , whereas at day 7 are considered as mature. One of the 7 days cell cultures was treated with drug A and another 7 days cell culture was treated with drug B for the entire experiment. The remaining two cell cultures (3 and 7 days) were remained untreated. One untreated cell culture was harvested after 3 days of growth, whilst the rest were harvested after 7 days of growth. At the end of this experiment, there were 8 RNA samples: SV3, SV7, SVA, SVB, BL3, BL7, BLA, and BLB . This procedure was repeated 5 times to obtain 40 RNA samples in 8 groups. Day 3 Treatment Strain 1 Strain 2 Untreated pre-mature SV3 BL3 Day 7 Untreated mature SV7 BL7 Drug A treated mature SVA BLA Drug B treated mature SVB BLB *each has 5 replicates I would like to compare the effect of different drug treatments on the two strains with untreated samples i.e comparison of SV3, SV7, SVA and SVB and BL3,BL7,BLA and BLB. I am trying to create a design matrix for the complete data set, but somehow I am mixing everything up. Can someone please help me with the with the correct construction of the design matrix. Best, Sanjana [[alternative HTML version deleted]]