Hi All,

If we have an design for which we have 4 groups, lets call:

1.Control Untreated
2. Control Treated
3. Cases Untreated
4. Cases Treated.

and we were interested in differences between:
-treated and untreated for Control
-treated and untreated for Cases
-treated differences between cases and controls
-untreated differences between cases and controls.
-differences between treated and untreated.

5 tests in total. We can then use edgeR contrast function as something like
this...

contrasts <- makeContrasts(
Case.TreatedvsUntreated = Case.Treated-Case.Untreated,
 Control.TreatedvsUntreated = Control.Treated-Control.Untreated,
 CasevsControl.Untreated = Case.Untreated-Control.Untreated,
etc..... levels=design)

This produces an appropriate rank order of significance for each contrast.
However, what is the cost of having no correction for the fact that I just
performed 5 tests on each gene instead of just 1 test??

Any insight?

Yours,

Michael

	[[alternative HTML version deleted]]

