Did anyone try pathway analysis with GAGE and Pathview using Sleuth results (
results_table.csv where column names are: target_id, test_stat, pval, qval, rss, sigma_sq, tech_var, mean_obs, var_obs, sigma_sq_max, smooth_sigma_sq, final_sigma_sq, degree_free, ens_gene, ext_gene)? I am following this tutorial https://www.r-bloggers.com/tutorial-rna-seq-differential-expression-pathway-analysis-with-sailfish-deseq2-gage-and-pathview/ but I have three samples with replicates (and more in future). I am able to get the pathways but not clear to which sample they belong to and also unable to get the figures showing up and down-regulated genes in the pathway. I think I need to troubleshoot the input for many samples with replicates.
I have posted details of my code and output at: https://github.com/pachterlab/sleuth/issues/91
Kindly guide regarding the input.