Table 3.
Types of microarray experiment designs using two colors. Ai: sample i from class A; Bi: sample i from class B; Ci: sample i from class C; R: reference sample. In reference design, Ai and Bi are labeled with Cy5, whereas R is labeled with Cy3. In the rest of the designs proposed, each class is labeled with a dye, typically Cy5 and Cy3 [49].
| EXPERIMENTAL DESIGN | ARRAY #1 | ARRAY #2 | ARRAY #3 | ARRAY #4 |
|---|---|---|---|---|
| Reference | A1/R | A2/R | B1/R | B2/R |
| Balance block | A1/B1 | B2/A2 | ||
| Incomplete block | A1/B1 | B2/C1 | C2/A2 | |
| Loop | A1/B1 | B1/A2 | A2/B2 | B2/A1 |