Hi, I am trying to perform a RNAseq analysis using DEseq2. My Experimental setup includes 8 different tissues with 2 genotypes each. I need to compare conditions within tissues and also tissues within genotypes. I tried using a ~genotype + tissue + genotype:tissue design but resultsNames(dds) only shows 16 coefficients and not all possible combinations, thus I can't select the comparisons I need for the results. In various posts, I read the suggestion to instead create a surrogate variable gentoype_tissue for each sample and use a simplified design formula ~genotype_tissue. I can now select every comparison I need using the contrasts. However, resultsNames(dds) still only gives me 16 coefficients and not all possible combinations. I would like to perform l2fc shrinkage for my results using the apeglm method, for which I need to use the coefficients which are not included for every possible combination.
Thanks a lot for your help, best Niko
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contrastsin the vignette.Thanks for your reply. Of course, I read the vignette, multiple times actually. Maybe I just don't understand how GLM work correctly... If I use a single combined group variable for the design
~genotype_tissueI don't understand why the coefficients don't yield all the different combinations. I must be missing something here... Thanks so much for your help, Niko