I am new to GSVA package. I am trying to the which geneset is differentially expressed in my samples? So, far i tried taking my differentially expressed genes as my input and my geneSets as reference file and ran gsva function opting "gsva" method of gsva() function. Next, to find which differentially expressed geneSets i am using limma approach and considering significant geneSets if corrected p value (FDR) is less than 0.2. Am i performing it correctly?
When I am using gsva function, there are three different methods we can use like "gsva", "ssgsea" and "zscore". Which one is more stringent way to use or which method is widely used one. I tried ssgsea and gsva both is giving me different results. I am just wondering which one to use?
If i use gsva method, it results me in both positive and negative enrichment scores if i use ssgsea method sometimes it yields me only positive values where gsva gave me both positive and negative enrichment scores. I am little apprehensive whether or not i am using the function correctly.
Any help would be really appreciated.