Contrasts table examples
Simple Contrasts file:
MutA-WT
MutB-WT
The Contrasts file is made on the basis of the Factors file, in this example:
| Experiment | Strain |
| WildType_rep1 | WT |
| WildType_rep2 | WT |
| Mutant_A_rep1 | MutA |
| Mutant_A_rep2 | MutA |
| Mutant_B_rep1 | MutB |
| Mutant_B_rep2 | MutB |
Example of the Contrast file using multiple factors:
To clarify multiple factors a little, we will consider a hypothetical experiment with three strains and two time points.
The factors are Strain (WT, MutA and MutB) and Time ( T1 and T2)
The Contrast file could be:
WT.T1-WT.T2
WT.T1-MutA.T1
MutA.T1-MutB.T1
MutA.T2-MutB.T2
This means that in the example above in total 4 analyses will be done, so 4 MA plots, 4 TopTables, 4 VolcanoPlots etc. will be generated
The Contrasts file is made on the basis of the Factors file, in this example:
| Experiment | Strain | Time |
| WildType_rep1 | WT | T1 |
| WildType_rep2 | WT | T1 |
| WildType_rep1 | WT | T2 |
| WildType_rep2 | WT | T2 |
| Mutant_A_rep1 | MutA | T1 |
| Mutant_A_rep2 | MutA | T1 |
| Mutant_A_rep1 | MutA | T2 |
| Mutant_A_rep2 | MutA | T2 |
| Mutant_B_rep1 | MutB | T1 |
| Mutant_B_rep2 | MutB | T1 |
| Mutant_B_rep1 | MutB | T2 |
| Mutant_B_rep2 | MutB | T2 |
To decide which contrasts should be made, we need to be clear what are our scientific hypotheses.
In other words, what are we seeking to show?
First, suppose that we wish to find genes that are always higher in Mutants than in Wild Type at T1 and T2.
Then we will need to form the four contrasts WT.T1-MutA.T1, WT.T1-MutB.T1, WT.T2-MutA.T2, WT.T2-MutB.T2, and select genes
that are significantly up for all four contrasts.
Or suppose we wish to establish that the difference between T1 and T2 is small compared to the differences between WT and Mutant.
An efficient way to establish this would be to form the contrasts (WT.T1+WT.T2)/2-(MutA.T1+MutA.T2)/2 and (WT.T1+WT.T2)/2-(MutB.T1+MutB.T2)/2.
reference: EdgeR user guide