Dear all, In our group we are moving from GenePix Pro (scanner and sofware from Molecular Devices) to Microarray Feature Extraction Software (scanner and software from Agilent) to analyze two color arrays from Agilent. We use limma and Rank Products for detecting differential expression. In our experience, for the same experiment (the same slides scanned and quantified with both systems): logRatios tend to be higher (absolute values) in Agilent than in GenePix log Ratio Standard Error measures tend to be higher in Agilent than in GenePix. We obtain less significant results with Agilent equipment than with GenePix (at the same FDR threhold). Our conclusion is that Agilent system is more sensible (actually its dynamic range is larger than GenePix) so small intensity differences are best detected than in GenePix scanner. As a result, the variability increases and the number of statistically significant genes decreases. I would like to know if any one have compared these two popular systems and if they had similar results. Thanks in advance. Best, Juan Carlos Oliveros, Ph.D.