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Old 01-22-2015, 11:11 AM   #7
Michael Love
Senior Member
Location: Boston

Join Date: Jul 2013
Posts: 333

> "Note that the comparisons to A don't require contrasts, since those are just fit coefficients."

Safest always to use contrast=c("condition","B","A"), because when we have expanded model matrices for symmetric shrinkage, then the coefficients are not B_vs_A, but simply A, B, etc. This will be clear from resultsNames(dds)

Last edited by Michael Love; 01-22-2015 at 11:24 AM.
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