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reactome / ReactomeGSA

R client for the REACTOME Analysis Service for comparative multi-omics gene set analysis
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Selected Pathways #63

Closed brookeabrown closed 1 year ago

brookeabrown commented 2 years ago

Hello,

Thanks for a great package and tutorial. When selecting for the relevant pathways to display in the heatmap, I am getting an error saying "Warning in plot_gsva_heatmap(gsva_result, pathway_ids = relevant_pathways, : Warning: No results for the following pathways: R-HSA-157118, R-HSA-9006934". However, other pathways I select are working fine, i.e. "R-HSA-177929","R-HSA-186797","R-HSA-201556","R-HSA-1227986","R-HSA-190236","R-HSA-5358351","R-HSA-2028269","R-HSA-74752","R-HSA-6806834".

Any idea why some pathways are giving an error? Does the function not check all Reactome pathways, or does it mean my dataset is not expressing the genes highly enough? For some of the pathways giving error, I know my dataset has at least some of genes expressed as measured from other analyses.

Thank you, Brooke

jgriss commented 2 years ago

Hello @brookeabrown,

Thanks a lot for your feedback!

I have to admit that I have not yet encountered this error before.

You can check all pathways present in your result object using the pathways functions.

Generally, we only return pathways that pass a minimal significance threshold.

Kind regards, Johannes