...
PCs | Batch | Center | Day | Month | Year | Amount | Concentr. | Row | Column | Stage | Grade | Age |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | 2.2e-16 | 2.2e-16 | 2.2e-16 | 2.2e-16 | 2.2e-16 | 2.2e-16 | 0.0004486 | 5.882547e-02 | 6.881028e-02 | 0.32 | 0.27 | 0.1071 |
2 | 0.5383 | 0.3486 | 0.5577 | 0.9876 | 0.2710 | 0.04873 | 0.6482 | 0.2862026 | 0.4786892 | 0.31 | 0.10 | 0.006634 |
3 | 0.04048 | 0.05258 | 0.03756 | 0.01480 | 0.1233 | 0.1786 | 0.5335 | 0.55585676 | 0.25289498 | 0.50 | 0.35 | 0.5131 |
4 | 0.0003439 | 0.01709 | 0.0008948 | 0.0001387 | 0.5725 | 0.7225 | 0.5267 | 0.0516508987 | 0.1404578746 | 0.43 | 0.43 | 0.02168 |
Finally, the center effect needs to go. Variables to adjust for: batch, center, plate row, plate column. Percent Variance explained after the adjustment:
It looks like removing the batch and the plate row did help some with the center effect but the plate column effect is still significantly higher. Need to remove that.
...
Now remove the batch, plate row and plate column, look at the percent variance explained:
Now the first principal component explains a little less than 15% of the overall variability. Correlation with the adjustment and bio variables, see if the center effect still present:
PCs | Batch | Center | Day | Month | Year | Amount | Concentr. | Row | Column | Stage | Grade | Age |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | 0.936 | 7.104e-05 | 0.881 | 0.915 | 0.938 | 0.780 | 0.027 | 0.998 | 0.757 | 0.36 | 0.22 | 0.6967 |
2 | 1 | 0.7801 | 1.00 | 1.00 | 0.96 | 0.92 | 0.75 | 0.97 | 0.45 | 0.36 | 0.30 | 0.02479 |
3 | 1 | 0.04068 | 1.00 | 1.00 | 0.93 | 0.97 | 0.51 | 1.00 | 0.18 | 0.30 | 0.27 | 0.1425 |