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New Analysis Example: Microarray Pathway Analysis - GSVA #343
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Based on a discussion with @cansavvy, the plan in the original comment above, and the training modules example for inspiration, the tentative plan for tackling this ticket is as follows:
Feel free to leave any suggestions/modifications you believe should be made before implementing this plan! |
You could also aggregate to the mean value for a gene symbol for each sample. |
What are the goals of this new example analysis?
ORA and GSEA are certainly popular pathway analyses methods, but GSVA requires a bit less cutoffs and decision making so having this method as an example would probably be helpful for our users.
Having a per sample pathway analysis results is a different question that GSVA can answer but the others can't so much.
What kind of dataset will this need?
We may want to use the same. original dataset we used in either GSEA or ORA so we have a comparison of pathway analyses?: GSE71270 (zebrafish CREB study) or GSE37418 (human medulloblastoma subtype).
What steps should be included in this analysis?
We can borrow some inspiration from https://github.com/AlexsLemonade/training-modules/blob/master/pathway-analysis/03-gene_set_variation_analysis.Rmd, keeping in mind that the narrative will need to change somewhat like other examples we've adapted from training to refinebio-examples: See #306
library(GSVA)
(add this to the Dockerfile)GSVA::gsva()
to perform GSVA, probably start out with largely the same parameters used in training but adjust if/when things look wonky.What packages/methods do you recommend using or looking into for this analysis?
Probably
GSVA
unless there are other package suggestions we should consider.The text was updated successfully, but these errors were encountered: