I am trying to run a differential analysis with EdgeR for 2 RNAseq samples, with only one condition (1 treatment, 1 control), and I only have 1 replicate of each, which I know is far from ideal.
Having reviewed the user manual, I've decided to use option 2 for this scenario (on pg. 23), where I will choose a reasonable BCV, and use that to run the exact test.
Unfortunately, I'm having a difficult time understanding what commands to run in order to do this, despite the example detailed in the manual.
After normalizing my samples, my effective libraries are as follows:
> ynorm$samples group lib.size norm.factors UWN_t2.bam 1 6411675 1.0307067 UMN_t2.bam 1 9047788 0.9702081
from reviewing the manual, I know I need to now set the BCV (with my chosen value of 0.2)
>bcv <- 0.2
but after that I don't know how to create a new DGEList which incorporates this new value, in order to run the exact test, since in the provided example there are some settings included that I cannot understand (size, mu, etc.).
Any advice would be greatly appreciated! Thank you,