[BioC] Re: raw intensities in affymetrix .cel files

[YUK FAI LEUNG]

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 at mcb.harvard.edu; yfleung at genomicshome.com
URL: http://genomicshome.com