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Summary of Methods
| Type of Experiment | Multiple Replicates? | Dye Swap? | Quantity of Interest | Mean Normalization | Variance Normalization |
| Sample 1 = Red, Sample 2 = Green | No | NA |  |
Equation (4) | Equation (5) |
| Sample 1 = Red, Sample 2 = Green | Yes | No |  |
Equation (4) | Equation (6) |
Sample  = Red, Sample  = Green Sample  = Green, Sample  = Red |
Yes | Yes |  |
NA | Equation (6) |
| Sample 1 & 2 = Red, Reference = Green | Yes | NA | M, Equation (7) | Equation (9) | Equation (11) |
