Hi everybody I'm using Affymetrix Genechip and I was wandering if it is reasonable to use a dataset whose genes belong to different analysis of the same experiment (a comparative analysis with three replicates). The genes belonging to all the analysis would compose the dataset to use for further analysis. I'd use the same bg correction and pm correct methods (RMA and subtractmm rispectively) but different normalization and summarization methods. For example 1st analysis bg correction :RMA normalization :loess pm correct :subtractum summarization :medianpolish 2nd analysis bg correction :RMA normalization :invariantset pm correct :subtractum summarization :liwong 3rd analysis bg correction :RMA ... If anybody could tell me what do you think about it I'd be very greatful. Thanks everybody