I try to analyze single sample gene set enrichment analysis on my data which is RNA-seq gene expression. I'd like to noticed that my data has got continous values not discrete or count.
After GSVA, number of the results I got were almost 400 gene sets with enrichment scores. Now, I am a bit confused whether I am on the right way of analyzing of single sample gene set enrichment for that data until this step. Also, I have searched some article about NES score but it was not clear for me. How can I interpret my results on these scores If I draw networks between pathways ? Like, some pathway are on/off for normal and disease. Because I do not think I will interpret it as up- down- regulated.
My second question, Is there any limitation (top and bottom) between these enrichment scores that are negatives and positives.
Also, I wonder the library of singscore but It is a bit complex and different with GSVA. Is there anyone who has used it for like this purpose before ? Thank you very much in advance.