As noted by @tjiagoM in #144 I was not extracting high weight genes based on standard deviation of the mean. Thanks for letting me know! :smile_cat: I was selecting extreme gene values from a different threshold. The top ranked genes were still selected, but several others were not.
This PR closes #144
I will need to file a followup pull request running the two updated files (results/high_weight_genes_node53_skcm.tsv and results/high_weight_genes_node66_skcm.tsv) through the pathway interpretation analysis (scripts/encoding_pathway_analysis.R).
The package I use for ORA (WebGestaltR) was recently updated (0.3.0) and updates are not straightforward (see greenelab/tad_pathways_pipeline#31)
As noted by @tjiagoM in #144 I was not extracting high weight genes based on standard deviation of the mean. Thanks for letting me know! :smile_cat: I was selecting extreme gene values from a different threshold. The top ranked genes were still selected, but several others were not.
This PR closes #144
I will need to file a followup pull request running the two updated files (
results/high_weight_genes_node53_skcm.tsvandresults/high_weight_genes_node66_skcm.tsv) through the pathway interpretation analysis (scripts/encoding_pathway_analysis.R).The package I use for ORA (
WebGestaltR) was recently updated (0.3.0) and updates are not straightforward (see greenelab/tad_pathways_pipeline#31)