I have been looking for some examples of limma with Affymetrix data. There is a simple example in the documentation, but not a case study as with the dye swap experiments, and I am confused as to how to proceed with using limma on my data. I need to eventually analyze a 2^4 factorial experiment, but I'd like to start with a smaller example so I can get the idea first. I know what contrasts are of interest to me, but I am unclear on how to use them with limma. ie. For a 2^3 factorial experiment: 3 Factors A,B,C ; each at two levels, high and low. Treat Factors ments A B C c low low low a high low low b low high low c low low high ab high high low ac high low high bc low high high abc high high high If I'm thinking about this correctly, the seven effects I'm looking for would be: Single: For A,B or C alone 2x interactions: AB, AC and BC 3x interaction : ABC With corresponding contrasts of: 4A = -c + a - b + ab - c + ac - bc + abc 4B = -c - a + b + ab - c - ac + bc + abc 4C = -c - a - b - ab + c + ac + bc + abc 4AB = +c - a - b + ab + c - ac - bc + abc 4AC = +c - a + b - ab - c + ac - bc + abc 4BC = +c + a - b - ab - c - ac + bc + abc 4ABC = -c + a + b - ab + c - ac - bc + abc I'm unsure how to proceed in getting significant genes from each contrast. Any help and/or references to examples etc. would be greatly appreciated! Thanks for reading this far! Stan Smiley stan.smiley@genetics.utah.edu 801-585-1527