An extreme form of the contingency table has only 2 classes per platform (ratios above and ratios below 1) and therefore only 4 cells.
This P-value can then serve as a measure for the position of each gene in the distribution of between-platform ratio differences.
However, the standardized difference and its P-value can be used as a measure for the position of a specific gene within the distribution of between-platform ratio differences and as such they can serve as a statistical threshold to determine which genes can be confidently interchanged between platforms.
For future research, the study suggested multiple ratios considered simultaneously may have higher predictive ability than single ratios which created a platform for multiple ratio models.
While oligonucleotide arrays measure the amount of mRNA in a single sample, gene expression data generated using cDNA array platforms are ratios of expression values in experimental samples over those in a reference sample.
We have used normalized microarray datasets (log2 intensity for single-channel platforms or log2 ratio in dual channel platforms) as published by the original studies.
However, because in each platform the observed ratio of 1 can be assumed to be true, the simplest function to scale the range of ratio of one platform to that of the other platform is a quadratic equation.
When comparing between the two platforms using tissue ratio data without regard for noise, the correlation between platforms is not very strong (r = 0.62, Figure 3A), similar to what was reported by Tan et al. 2003 [ 7].
Both platforms produced the same results, but the nominal logistic regression platform provided odds ratios and their confidence intervals, while the generalized linear model platform facilitated tests for overdispersion.
Due to the technological difference in experimental design between Affymetrix (intensity) and Agilent 2-color (ratio) platforms, three analysis configurations (ACs 1-3, inlustrated in Figure S1) were designed to ensure that both datasets matched in comparison.
Non-Affymetrix platform data were ratio-normalized, and Affymetrix raw CEL data were MAS5-normalized.
