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Removing the batch effect didn't completely remove the center and the row/column effect. Day, month and year of shipment have been taken care of. Next remove the batch the the plate row effect. We identified with Justin the the entire 0652 batch doesn't have any plate row or column information:
| Code Block |
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> table(batch, adj$plate_row)
batch A B C D E F G H
0359 5 5 5 5 5 5 4 4
0402 5 4 4 5 5 5 4 4
0432 6 5 5 5 6 5 6 5
0460 6 6 6 6 6 6 6 5
0475 6 6 6 6 5 6 6 5
0501 3 3 3 3 3 3 2 2
0536 6 6 6 6 6 6 6 5
0563 6 6 6 6 6 6 6 5
0581 6 6 6 6 6 6 6 5
0652 0 0 0 0 0 0 0 0
0667 6 6 6 6 6 6 5 5
0708 6 6 6 6 5 6 5 5
0807 1 0 0 2 0 1 0 0
> table(batch, adj$plate_column)
batch 1 2 3 4 5 6
0359 8 8 8 8 6 0
0402 8 8 6 8 6 0
0432 5 8 7 8 8 7
0460 8 8 8 8 8 7
0475 8 8 7 8 8 7
0501 8 8 6 0 0 0
0536 8 8 8 8 8 7
0563 8 8 8 8 8 7
0581 8 8 8 8 8 7
0652 0 0 0 0 0 0
0667 8 7 8 8 8 7
0708 8 7 7 8 8 7
0807 2 1 1 0 0 0
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We decided to remove the patients from the batch 0652 from further analyses (43) and work with a smaller dataset (468 patients):
| Code Block |
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> 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(redB[,mask])
> redBR<- redB[,mask] - t(X %*% Xbcrw)
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