I have RNA-seq dataset from two population and two conditions as recently posted in https://support.bioconductor.org/p/123895/#123921. I've successfully performed the evaluation of difference between two groups in gene expression changes thanks to you.
Then, I have done pathway analysis based on fold change between two conditions using gage with reference to KEGG pathway.
It seems that there is difference between two groups in pathway analysis results (i. e. some pathway is upregulated by condition change in one group, but not changed in the other group). I would like to evaluate which pathway is significantly different between groups. Does someone knows how to evaluate it with statistically valid method?
Thanks in advance for your help.