I usually analyse data with DEG I've got, and it is my first time using GAGE to analyse my data.
I took the output of DESeq2 (log2FoldChange) as input, and made a list of keggID-Geneset since there is no appropriate dataset in package suitable for my data.
I didn't get any significant result (q-value<0.05). It seems so strange, since I can get a several significant KEGG pathway while using DEGs. I wonder if my codes are wrong.