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.
2 answers
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)
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.
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