Hi everyone it is not clear to me what is the difference between results(dds, contrast=list) and results(dds, list) i have been scrutinizing the online tutorials for some of the multifactorial designs for example here: https://rstudio-pubs-static.s3.amazonaws.com/329027_593046fb6d7a427da6b2c538caf601e1.html#example-4-two-conditionss-three-genotpes-with-interaction-terms they use results (dds,list) to compare mutant-treatment vs WT-treatment in a 2x2 design (mut vs wt) (treated vs control) with the following

res = results(dds, list( c("genotype_MU_vs_WT","genotypeMU.conditionTrt") ))

i was curious- are results (dds, contrast=list()) the same? let's say for the example of comparing mutant -treatment vs WT-treatment comparison

In R, if you don’t name arguments (eg contrast=...) then it follows the order of the arguments in the function definition. The second argument is contrast, so there is no difference.