I am basically a biologist and very new to RNASeq/bioinformatics. We just got our RNASeq results. We had two groups. Cells infected with virus and uninfected control group (n=3 for each group, biological replicates). Our infected vs control are not separating in 2 distinct groups when PCA is performed. There are no DEGs when adjusted P values are considered. P values are significant and there is log2 fold change for some genes. Using the same gene list, I ran GSEA (using galaxy server, standard parameters) and found some enriched hallmark pathways with significant adjusted p value.
I am totally confused if this all is making sense at all? Should i consider my GSEA results reliable?
Again, I am very new and might need a very basic explanation to understand what is happening here.