probably someone has already raised this question. How large the size of a gene set to be used as an input for fgsea or another gsea analysis?
I use GO biological process from Msigdb collection and it seems that it has larger gene sets (7529 gene sets, I believe).
when I run the fgsea analysis and set them into minSize 15, maxSize 500, and nperm 1000, I did not find any significant pathways (adjusted p value < 0.05). However, once I increased the permutation to 10000, I saw that there were 277 significant pathways.
I am just wondering whether it was a good idea to increase the permutation as a way of compensating larger dataset such as GO biological process? or should I just set a more stringent minSize and maxSize parameter?
Kindly provide any information about this.
Thanks in advance.