Error: Pathway analysis using Sleuth results

Question

[bioinfo8]

Hello,

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.

Thanks!

Answer 1

[bigmawen]

pathway graphs without data mapped is because that no gene (or compound) IDs can be mapped to the pathways. This is most likely because that gene.idtype (or cpd.idtype) is the not set correctly or gene.data (cpd.data) is not in the right format. The error messages are consistent with this. Please check help info for pathview function:
?pathview

if you have any unknown problem in R, you may also use the pathview web server:
https://pathview.uncc.edu/