Hello everybody,
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 :-(
Sorry for stupid question.
Paul.
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'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.
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Hi Devon,
wau nice explanation. So in your example we have 20 replicates and 2 conditions, am I right? Thank you!!
Paul.
10 replicates. When thinking of replicates, the numbers should be per group. This can become more difficult in situations where there are multiple conditions (suppose some of the mice were males, others were females, some wild-type, others had a mutation and that these weren't evenly distributed) such that a single number doesn't describe the whole experiment, but the general principal still apples.
BTW, a condition can also be continuous, such as age or height or income, so don't be mislead into thinking only in terms of strict groups or factors. This is often called a "covariate", but at the end of the day it's the same thing (it also serves the same purpose in the underlying math).