[BioC] DESeq2 - experimental design

Claudia Pommerenke claudia.pommerenke at med.uni-goettingen.de
Wed Mar 26 12:41:49 CET 2014

Dear Michael,

I have been switching from edgeR/DESeq to DESeq2 and I'm happy to 
include more complex experimental design to the analysis. Thanks for 
developing and providing this R-package! :o)

I hope I can bother you with some questions about your package:
1. when analysing for let's say two variables (e.g. ~ type + condition), 
will this be a difference to change the order of the variables (~ 
condition + type)? Probably this will do a blocking and hence order is 
important here similar to edgeR?
2. For more than 2 variables (e.g. ~type + condition + time) would this 
be meaning blocking will also be done for the further variables (e.g. 
type for time)? If I intend no blocking I probably need to do ~ 0 + type 
+ condition + time?
3. Is it also possible to study nested effects and other interactions 
(e.g. condition:time)?

I would be happy getting any answer of you.
Thank you,

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