Table 2 Observed agreement and p-value for each pairwise comparison within each platform using the weighted kappa statistic. Print-tip loess normalized Cy5 intensities were used for both two-channel arrays; MAS5.0 expression summaries were used for Affymetrix GeneChips.
From: Application of a correlation correction factor in a microarray cross-platform reproducibility study
Chips compared | Observed Agreement | P-value |
|---|---|---|
GMU | Â | Â |
   1420 v 1421 | 71.89% | < 0.0001 |
   1420 v 1422 | 66.31% | < 0.0001 |
   1421 v 1422 | 75.41% | < 0.0001 |
C3B | Â | Â |
   7–7 v 8–22 | 28.18% | 1.00 |
   7–7 v 8–31 | 51.82% | < 0.0001 |
   8–22 v 8–31 | 29.14% | 1.00 |
Affymetrix | Â | Â |
   QAQC8 v QAQC10 | 89.75% | < 0.0001 |
   QAQC8 v QAQC13 | 89.54% | < 0.0001 |
   QAQC10 v QAQC13 | 89.57% | < 0.0001 |