Affymetrix Genechip Microarray

Analysis of expression data includes the process of scaling. In this process the average intensity value is scaled relative to a common target intensity value enabling data from different chips to be compared. For example, if the average intensity value of chip 1 is 200 and that of chip 2 is 300, without scaling the two chips to a common value, chip 2 is always likely to give higher expression levels than chip 1.

The differences in initial intensity values are usually due to assay variables such as pipetting errors that are independent of the relative transcript concentration. All of the chip sets that were used in the experiments described in this chapter were scaled using a scaling factor of 250, as recommended by Affymetrix for the AtGenome1 GeneChip. Single array analysis is then performed. This process allows the creation of gene expression data matrices. These are used for subsequent classification of changes in gene transcription levels, and for procedures such as gene clustering.

The data from single array analysis is stored as a .chp file, which is created from the .cel file. Single array analysis creates a signal value for each probe cell that is a measure of the abundance of the transcript. This analysis generates a detection p-value, which is used to give a detection call for each probe.