I'm working on a gene expression file from an RNA seq experiment and try to compare between two groups of samples. I'm pretty new to this world of gene expressions and need some help. I have a strong reason to believe that there should be a biological difference between the two groups (from the biological aspect). When I do different gene expression I get many differentially expressed genes and when I cluster the samples according to the genses, I don't see two clear separation between the groups. Is there a way to filter the genes I get from my differential expression algorithm so I can see a better clustering effect? I am interested in selecting genes from the list of differentially expressed genes that will separate the two groups in the best way, however, there are so many genes that are differentially expressed that I don't know how to effectively do it. Also, I have been trying two different differential gene expression methods (ttest and limma) and the genes I get from each limma don't appear in the gene list I get from the ttest. Which one should I use?
Thanks a lot!