Hi. In my experiments I have control and stimulated cell cultures for individuals with and without disease (usually no replicates, but sometimes up to 3 replicates). Therefore I have two M vs A plots, control verses stimulus for the disease group, and control verses stimulus for the group with no disease. For each group, I analyse Affy data with rma and generate M vs A plots. I define everything with M value > 0.45 (in a 2 chip comparison) as differentially expressed, but some genes are differentially expressed in the disease and no disease groups, but at a much higher level in one of the groups. Currently since I define the noise as m = 0.45, I just simply subtract the m values for any gene which is differentially expressed in both M vs A plots, and if the difference is greater than 0.45 I call that different between both groups. 1) Is this correct? 2) Does any one know how many false positives to expect in two chip comparisons with Affy chips Regards Anthony -- ______________________________________________ Anthony Bosco - Cell Biology Research Assistant Institute for Child Health Research (Company Limited by Guarantee ACN 009 278 755) Subiaco, Western Australia, 6008 Ph 61 8 9489 , Fax 61 8 9489 7700 email anthonyb@ichr.uwa.edu.au