Dear All,

I have problems in understanding what is the interpretation of default
output of interaction contrast and how can I change the default settings
(resultsNames(results)) and explore other interactions?
For example, here are the 3 factors I am interested in:
1. treatment; levels: disease and control
2. localization; levels: A and B.
3. sex; levels: male and female

If the design1 is: ~sex + treatment*localization, by default, the reported
contrast in the results is:
Wald test p-value: treatmentdisease.localizationA.
Q1: Can I interpret the output as a list of genes that are diff.expressed
(DE) between localization A and localization B in a disease?
Q2: How could I get the DE genes between localization A and localization B
in a control? Or DE genes between disease and control for localization A?

If I change the order of factors in a design:
design2=  ~sex + treatment*localization, then by default in the results I
get
Wald test p-value: localizationA.treatmentdisease. Can I interpret this as
a list of DE genes between disease and control in localization A? I tried
it, but the results were the same as ones got from design1.

Thank you in advance for your help.
Best,
Mike

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