Table 2 The numbers and proportions of probe sets with significantly different expression levels between parental pairs, fold change in expression levels between parents at a false discovery rate of 0.15, and numbers of genes expressed only in one genotype of each parent pair.
Method | Parental comparison | Differentially expressed genes | Genes with higher expression in first parent of pair listed in second column | Fold change of all differentially expressed genes | Genes with >2 fold change | Genes present in one parent and absent in the other | ||||
|---|---|---|---|---|---|---|---|---|---|---|
| Â | Â | no. | no. | % | minimum | median | maximum | no. | no. | % |
MAS | P1 vs P2 | 7062 | 3814 | 54.0 | 1.17 | 1.92 | 711 | 3196 | 420 | 5.9 |
| Â | P1 vs P3 | 7227 | 3608 | 49.9 | 1.16 | 1.95 | 1141 | 3385 | 480 | 6.6 |
| Â | P2 vs P3 | 4222 | 2009 | 47.6 | 1.18 | 1.92 | 324 | 1960 | 329 | 7.8 |
RMA | P1 vs P2 | 12627 | 6752 | 53.5 | 1.04 | 1.41 | 312.3 | 1890 | -- | -- |
| Â | P1 vs P3 | 12821 | 6538 | 51.0 | 1.05 | 1.41 | 180.8 | 2039 | -- | -- |
| Â | P2 vs P3 | 8147 | 4028 | 49.4 | 1.03 | 1.40 | 175.6 | 1179 | -- | -- |