I have a question regarding how to set up model matrix for my data frame in edgeR.
The complete steps from reading counts table after mapping till setting up model matrix is given here http://rpubs.com/upendra_35/7800
So basically in the dataframe i have two genotypes, two treatments and 7 tissues and if i am interested in looking for all those differentially expressed genes for each of the individual tissue, which of the two model matrix should i use?
design <- model.matrix(~gt * trt)
design <- model.matrix(~group)