hi Claudia,



On Thu, Mar 27, 2014 at 5:17 AM, Claudia Pommerenke <
claudia.pommerenke@med.uni-goettingen.de> wrote:

>  Dear Michael,
>
>
> My understanding from working with the edgeR package is, that you can
> consider paired samples or batch effects when comparing two or more
> treatments. Accounting for paired samples seems to be a specific case of
> "blocking" in experimental design. In edgeR doing  ~type+condition I can
> retrieve the 'condition' comparison including the correction for the paired
> effect 'type'. Is this also true for DESeq2? And if so, does the order
> matter in the formula e.g.: ~type+condition the same as ~condition+type?
>
>
>
​Yes, using a design formula '~ type + condition' allows you to retrieve
the condition comparison correcting for the type effect.  This is generally
true of linear models and generalized linear models (we call this
"multi-factor design" in the vignette, and it was also implemented in the
previous DESeq as nbinomGLMTest). The order only matters in so far as I
mentioned in my previous email.

Mike​

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