Hi,

Suppose that in my expression matrix I have 3 conditions: treatment A, treatment B, and control (2 replicates everywhere). Now my goal is to compare treatment A to control. My question is, should I do voom and further analysis on the whole expression matrix (with the appropriate contrast matrix) or should I first take a subset of the expression matrix with the columns only for treatment A and control (and then do voom and other steps)? Will there be any difference?

Thank you

This question comes up fairly often, although admittedly not the easiest to search for.

The general advice is that unless you have a very good reason not to, you should run the fit and eBayes step on all of the data, and just make sure you specify your contrasts correctly so that you get the statistics for the correct hypothesis you want to test.

Here are some related threads:

1. https://support.bioconductor.org/p/61556/
2. https://support.bioconductor.org/p/88032/
3. https://support.bioconductor.org/p/60556/

FYI, when you want to search the support site for previous related questions / discussions, you may have more luck by using Google to search and ensuring it restricts results to this website by adding site:support.bioconductor.org to the end of your query.