Error: Pathway analysis using Sleuth results
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bioinf ▴ 10
@bioinf-12080
Last seen 6 months ago
United States

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!

pathview gage rna-seq R sleuth • 1.1k views
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theobroma22 ▴ 10
@theobroma22-11920
Last seen 4.9 years ago

It seems the error is that your keggresids are not used as the keynames, or keys argument used to 'select' these from your object in order to map them to the pathway map. Can you label your arguments so that it's easier to read your code? 

And did you forget to include the target_id column? 

 

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@theobroma22: Thanks for the reply. I have added and updated labels for some of the arguments.

Regarding target_id column, I have used it here: `Changed gene.data=qval.e to gene.data=lrt_results.e.noNA'

 

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Luo Weijun ★ 1.5k
@luo-weijun-1783
Last seen 5 months ago
United States

if you got pathway graphs with no color, then your data were not mapped to the target pathways. It could be that you specify the wrong species or gene ID, or your data are in the wrong format.

First of all, your species is Rrr, what’s that, this is not a KEGG species! Your gene ID map used some package org.Rrr.eg.db, which is not a Bioc package either. Please make sure you get these problems fixed first, and follow GAGE/Pathview workflow correctly.

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@Luo Weijun: Thanks for the reply. I am able to get the pathways (so species has no issues) but not clear to which sample they belong to and also unable to get those figures showing up and down-regulated genes (with colours) in the pathway (I am getting pathway figures). I am trying to troubleshoot the input for many samples with replicates, but still not successfull.

I know Rrr is not a species name, I am using a hypothetical name here.

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