Expression analysis overview:

From labeling to hybridization  >>  Probeset overview

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Probeset design:

A single transcript is represented by "probe pairs" spanning 600bp upstream the 3' end of the consensus sequence.
Every "probe pair" is made of two 25-mer oligonucleotides, one representing the perfect-match sequence for a defined transcript (PM) and another identical but containing a single mismatch nucleotide at the 13th base(MM), which will be used to assess specificity of hybridization.


cell >> probepair >> probeset >> GeneChip array

    
Pre-processed GeneChip image :

Upon GeneChip surface scanning, emission intensities for every cell in the array are collected.
The ".DAT file" is the image of the array surface acquired by the GeneArray scanner at 2.5 µm/pixel resolution.
    
Post-processing GeneChip image :

The ".CEL file" is calculated from the corresponding .DAT file.
For every cell element, peripheral pixels are eliminated from further analysis; intensities for the remaining pixels are averaged and the resulting intensity value is assigned to that cell. The .CEL file, therefore, represents an elaborated version of the image.