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gabrielodom / pathwayPCA

integrative pathway analysis with modern PCA methodology and gene selection
https://gabrielodom.github.io/pathwayPCA/
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Re-run Ovarian PNNL data with CP:KEGG and C6 Oncogenic Signature #27

Closed gabrielodom closed 5 years ago

gabrielodom commented 6 years ago

Check pathway significance for these two pathway collections. For links, see LWTest/Summary - Pathway PCA_9-4-2018.docx.

gabrielodom commented 5 years ago

Results are in LWTest/different_pathway_collections_testing.html.

The CP:KEGG pathway collection returned two significant pathways:

The Toll Receptor pathway was also the pathway with significant results when using Wikipathways.

The C6 pathway collection returned 0 significant pathways. I wonder if this is because these pathways are all biologically correlated.

Supervised PCA also returned 0 significant pathways from either collection.