Understanding the "relativeness" in RNA seq experiments Let's say we have two samples, sample 1 and sample 2, and we're running an RNA seq experiment. Consider genes A and B for both. For simplicity, let's say that when we run the RNA seq experiment, we get the following results:

gene A sample 1 count: 2

gene B sample 1 count: 4

gene A sample 2 count: 2000

gene B sample 2 count: 4000

Based on my understanding, RNA seq gives relative results. So I guess in this guess, how can you tell whether either one of the following are true:

1- You sequenced sample 2 a thousand fold more compared to sample 1

2- Sample 2 really has a thousand fold more expression in both genes A and B
We cannot be sure about this. For all we know, they could have been sequenced to the same depth and there is a biological difference that drives the 1000x (ridiculously large) fold change.
See above


The only thing you can say for sure is that gene B is expressed twice as much as gene A in samples 1 and 2. That's what "relative" means - relative expression of genes within a sample.