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| Code Block |
|---|
> mask<-batch!="0652" > length(mask) [1] 511 > table(mask) mask FALSE TRUE 43 468 > X<-model.matrix(~factor(batch[mask]) + adj$plate_row[mask]) > Xbcrw<-solve(t(X) %*% X) %*% t(X) %*% t(redBred[,mask]) > redBR<- redBred[,mask] - t(X %*% Xbcrw) |
Percent variance explained after removing the batch and the plate row effects:
The first principal component is smaller but not significantly so. Lets look again at the variables:
PCs | Batch | Center | Day | Month | Year | Amount | Concentr. | Row | Column | Stage | Grade | Age | ||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 | 0.7905 | 0.0001809 | 6.9e-01 | 8.4e-01 | 8.2e-01 | 6.4e-01 | 9.7e-02 | 9.9e-01 | 1.2e-05 |
| | 0.41 | 0.53 | 0.6716 |
2 | 1 | 0.7522 | 1.00 | 1.00 | 0.96 | 0.93 | 0.75 | 0.96 | 0.46 |
| | 0.36 | 0.30 | 0.02475 |
3 | 1 | 0.03907 | 1.00 | 1.00 | 0.93 | 0.97 | 0.52 | 1.00 | 0.17 |
| | 0.30 | 0.27 | 0.1425 |