How To Calculate/Implement Gene Set Enrichment Analysis

Question

[jack]

Hi all,

I have following inputs and I want to implement gene set enrichment analysis . would someboy help me how can I implement it in R ?

a vector with significance values : (0.02,0.01,0.05,0.44,0.03,..) and vector with pathway: (1,0,1,0,0, ...) and I want to use 100 permutation test.

Answer 1

[Michael]

Try existing implementations. Here is the GSEA BioC view: http://www.bioconductor.org/packages/release/BiocViews.html#___GeneSetEnrichment (GSEABase: http://www.bioconductor.org/packages/release/bioc/html/GSEABase.html)

Answer 2

[Sean Davis]

There are many implementations of gene set analysis in R/Bioconductor, so I, like Michael, would suggest starting with some quick searches before implementing on your own. The limma package offers several implementations itself.