How can I generate list of genes in R?

Question

[rufusek500]

Hello, I am wondering how can I generate both list of genes which are upregulated and list of genes which are downregulated after the normalization, but before the clustering, because I want to generate list of genes between my control samples(15) and infected samples(12), should I use the function so called "geneList"?

[ATpoint]

It's unclear at what step you are. What are your dat? Did you map/quantify them already and have a count matrix, if so the DESeq2 manual is a good start.