GeneChip array data

Methods

Each workstation running Affymetrix Microarray Suite can control one scanner. Each probe array is scanned twice, taking up to 10 minutes, depending on the array format. The software calculates an average of the two images, defines the probe cells & computes an intensity for each cell. The double scan improves assay sensitivity & reduces background noise.

Each complete probe array image is stored in a separate data file identified by the experiment name & is saved with a data image file (.dat) extension.

Data is analyzed using the Microarray Suite Expression Analysis software. The *.dat image is analyzed for probe intensities according to the algorythm defined in the exeriment information file (*.exp). This generates the cell intensity file (*.cel). The analysis output or chip file (*.chp) is generated from the cell intensity file (*.cel). Results contained in the analysis chip file (*.chp) are automatically displayed in a specific analysis window.

*.dat file

compute cell intensities ->

*.cel

analyze cell intensities ->

*.chp ->

data output