Table 3. Augmented ANOVA table for Individual-Centered PCA of SNP data on oats, using SNP coding rare = 1.
PCA is applied to SNP main effects and S×I interaction effects combined (S&S×I), and the portion of each is shown in the last two columns.
| Source | df | SS | SNPs | SxI |
|---|---|---|---|---|
| Total | 851534 | 157442.756 | ||
| Individuals | 634 | 2077.808 | ||
| S&SxI | 850900 | 155364.948 | 16872.731 | 138492.217 |
| PC1 | 1974 | 17402.420 | 16734.514 | 667.906 |
| PC2 | 1972 | 15564.018 | 21.919 | 15542.099 |
| PC3 | 1970 | 9476.489 | 40.283 | 9436.206 |
| PC4 | 1968 | 5781.809 | 23.612 | 5758.197 |
| PC5 | 1966 | 4758.747 | 25.746 | 4733.001 |
| PC6 | 1964 | 3482.969 | 5.452 | 3477.517 |
| PC7 | 1962 | 2970.194 | 4.894 | 2965.270 |
| Residual | 837124 | 95928.303 | 16.312 | 95912.021 |