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.
Kind of, typically one uses a negative binomial, which allows for replicates. If one wanted to do use a Fisher's test (don't do this) then the second row would be the total counts in the sample excluding those for the given gene being examined. But really, you need biological replicates, so just use one of the many (Bioconductor) packages that already allow for this.