Hi Yi,
The colour you are seeing comes from the pre-whitening performed to correct for different variances in the 2 groups. This corrected is implemented as a filter that is used to pre-multiply the data and the design, leading to the change in values. You can verify this by switching the variance option to "equal". Not that I would recommend this, but it should show you where the change is coming from. Basically, don't worry about it!
Best wishes,
- Martyn
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