In RNA-Seq analysis it is common to use tests analogous to Fisher's exact test to evaluate whether a gene is differentially expressed in two measured conditions.
Fisher's exact test relies on compiling a 2x2 (or greater) table of outcomes x conditions. When applied to RNA-Seq, I was wondering what the 2x2 table consists? I would assume that the two different genes are the two columns, but what then are the rows? The actual data and the average read count in each condition, to test the gene versus a null hypothesis of random sampling of read counts?
I would be happy for help clarifying this issue.