I'm performing a RNA-seq analysis using DESeq2 and I'm wondering what is the correct analysis approach for my multifactor design. We have searched different posts in different forums and I can't figure out how to approach it.
Here I paste my multifactor design:
Using a ~batch + condition design, we obtained the following error:
some variables in design formula are characters, converting to factorsError in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified. One or more variables or interaction terms in the design formula are linear combinations of the others and must be removed.
We have also checked DESeq2 multiple factors nested design and we are still obtaining the same error. What is the correct factor design for this experiment?
Thank you so much for advance, David.