Hi everyone! I have a problem understanding the protocol of edgeR, where a batch effect is adjusted in differential expression analysis (4.2.8).
I have also a batch effect in my samples and I have constructed the design matrix like this:
> design conditionControl conditionMorphine batch2 C_P1_54 1 0 0 C_P1_55 1 0 1 M_P1_60 0 1 0 M_P1_61 0 1 1 attr(,"assign")  1 1 2 attr(,"contrasts") attr(,"contrasts")$condition  "contr.treatment" attr(,"contrasts")$batch  "contr.treatment"
Is this correct?
Moreover, I have followed the example of edgeR protocol from the top to the final step, but I don't understand how the batche effect is taken into account in the final contrast. It says "First we check whether there was a genuine need to adjust for the experimental times. We do this by testing for differential expression between the three times. There is considerable differential expression, justifying our decision to adjust for the batch effect:" And then "Now conduct QL F-tests for the pathogen effect and show the top genes. By default, the test is for the last coefficient in the design matrix, which in this case is the treatment effect:" So am I correct thinking that in the second test the batch effect is taken into account even if we don't add it to the commandd? The fact that we have been including it during all the analysis makes that the values are already adjusted? Or am I missing something important?
Thanks in advance