Parameters Used for Data Analysis
| Parameter | Description |
| Average difference[i] | Average of the differences in intensity values between the perfect match and the mismatch oligonucleotides over the entire probe set for one gene (arbitrary units) |
| Average difference change[i] | Average difference (induced)—average difference (control) |
| Difference call[i] | Five possible values: D = decreased; MD = marginally decreased; NC = not changed; MI = marginally increased; I = increased |
| Fold change[i] | Permits the symmetrical expression of the fold change as a positive number when the transcript has increased over its baseline state, and as a negative number when the transcript level declines. Corresponds to average difference (induction)/average difference (control) for induced and average difference (control)/average difference (induction) for repressed genes. For weakly expressed genes, values are corrected for noise. |
| Change factor | For increased intensity: fold change − 1; For decreased intensity: fold change + 1 |
| Sort score[i] | Quality measure based on fold change and average difference change |
| Purity | (# pairs used − least (# of pairs called increased, # of pairs called decreased)*2)/pairs used |
[i] Output from the Affymetrix GeneChip software.