Thanks. I glance the whitepaper before. But it doesn't mention the bit I want. In page 4 of the paper it says: A note about .CEL Files The Statistical Algorithms begin with information contained in the .CEL file generated by Microarray Suite software. The .CEL files contain a captured image of the scanned GeneChip? array and calculations of the raw intensities for probe sets. The me thod for calculating individual cell intensities, thus generating the .CEL file, is not affected by the Statistical Algorithms. Therefore, it will not be discussed here. I vaguely remember that the software discard the outermost pixels from a feature and use the 75% in the rest as the raw feature intensity. Is it correct? Is there any other thing being done on the raw data? Regards, Fai -- Yuk Fai Leung Department of Molecular and Cellular Biology Harvard University BL 2079, 16 Divinity Avenue Cambridge, MA 02138 Tel: 617-495-2599 Fax: 617-496-3321 email: yfleung@mcb.harvard.edu; yfleung@genomicshome.com URL: http://genomicshome.com