I want to conduct a differential expression analysis over bulk RNA-seq data, using the limma package. There are several guides for this package, but non of them is helping me get good results, I don't know if I'm doing something wrong or what.
Some functions are not very clear whether I need to use them are not, like
DGEList for example (I didn't understnad what do I need it for). Plus, how to build the design & contrast is still unclear for me.
The analysis is between two groups, based on one factor only: Response to treatment vs No Response.
Can someone please suggest the best and most recommended guide? plus, suggestions of which functions should'nt be used, and how to build contrast / design matrices, would be more than welcomed and appreciated.