<p>Hello everybody,</p>

<p>can somebody explain me what is the difference between replicates and conditions in RNA-seq? I found those terms in TopHat, Cufflinks and CummeRbund, but I do not understand it very well :-(</p>

<p>Sorry for stupid question.</p>

<p>Paul.</p>

<p>These terms will be common in all of science and might best be illustrated with an example. Say we have 20 mice and we evenly divide them into two groups of 10. In the first group we administer some sort of drug via injections while in the second group we administer a placebo. We then extract RNA from some tissue and analyse it (presumably via RNAseq, but the method and material don&#39;t matter). The RNA from the individual mice in each group would be replicates. The groups themselves represent different conditions (drug vs. vehicle/placebo). The terminology is the same regardless of material and also holds outside of biology.</p>
