Hi, we have been using GSEA to analyze 7 tumor and 7 matched normal tissue.(RNA seq) Our team divide 7 tumor samples into 2 group, Group A, Group B. So the cls file contains 3 types( Normal, Group A, Group B) and ran two comparison 1) GroupA vs Normal, 2) GroupB vs Normal.
Can we use the NES score that we obtained from each comparison and subtract the scores for the hallmarks that both were enriched in GroupA and GroupB. For example, the NES score of EMT for Group A and B was 2.62, 1.33 relative to normal individually and the NES score of Inflammatory response was 1.95, 1.31 .(identical expression value of normal) So, by subtracting 2.62-1.33= 1.29(EMT) and 1.95-1.31= 0.64(Inflammatory response), we could conclude that 'EMT' was more highly enriched in Group A compared to 'Inflammatory response' relative to Group B.
The reason we didn't just use Group A vs Group B comparison is beacuse we wanted to include the information of Normal tissue.
Thanks in advnace for your advice.