Hello, 

In a multi-factor DESeq2 design, it accounts for the changes in one group while testing for changes in others. In section 1.5 of the vignette for example it controls for type while testing for differences in condition. I assume it calculates a normalization factor + size factor and then adjusts the counts accordingly?

In that example in the vignette is it possible to access the counts which have been normalized for type and size factor? 

Thanks

You're right than size factor/normalization factor (s_ij) and the factor effects are similar, we have (for a standard model):

log(E(count)) = s_ij 2^(beta_intercept + beta_type + beta_cond) (1) 

so we could also rearrange terms and write this:

log(E(count)) = s_ij s_type 2^(beta_intercept + beta_cond) (2)

...where s_type = 2^beta_type.

But in the software and model, we keep the type effect in the exponent, as in (1). 

I have it on my list of todos, to allow for easier plotting of normalized counts, removing the calculated group/batch effects (like "type" here), to make it easier to see the condition effect for example. But this is not yet implemented. I'll ping this thread when I've added something to the devel branch.