Dear Limma/EdgeR users,
I have 2 treatment groups, 3x biological replicates for each. I also have 2 extra samples, a pool of each treatment group.
I am comparing a "vanilla" analysis with the biological replicates, to an analysis with the pooled samples. I.e 1 vs. 1 sample.
In the EdgeR manual, there are 4 clear ways/examples of how to do an analysis without biological replicates. This has been very useful, and there is no problem; great.
However, reading about different methods for RNAseq differential gene expression has suggested the voom - lmma is a more robust approach. E.g. less susceptible to the mean - variance relationship.
In addition, a recent publication also promotes the use of voom-limma over other methods due to False Positive Rates.
Bearing that in mind, I want to compare using the biological replicates to using the pooled samples alone with voom-limma, as I am able to do with EdgeR.
Is there a way for voom-limma to "learn" the variance/dispersion/weights etc from the biological replicates I have, and then use them with the pooled samples alone?
Thank you very much.