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Enrichment Score Calculation In Bioconductor

Hi: I have a set of gene signatures obtained by SAM that contains data like this:

Gene ID     Score (sd)   
123456_at      45,5655
.......              ........

where Score is the t-statistics obtained.

The question that I have is based on that data, how I can obtain the enrichment score using bioconductor?

bioconductor enrichment
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updated by seidel seidel • written by Layla • Layla

Hi Marco Aurelio. Enrichment score of what? Do you mean GO term enrichment analysis? KEGG pathway enrichment analysis? Do you just want the p-value of your score? Try to be a bit more specific, and it will be easier to help you.

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written by miquelduranfrigola miquelduranfrigola

I want to compare this list of genes with a data matrix that contains a set of probe sets ordered by their differential expression between healthy and disease samples.

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written by Layla • Layla

If I have the set of up and down regulated genes as a signature from SAM, how can I compute an enrichment score for these genes, if I have only the t-statistics? thanks

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written by Layla • Layla

1 answer

You could try the geneSetTest() function in the limma library (available at bioconductor). Given that you have gene signatures (i.e. a group of genes), and a healthy/disease data set, you can test your gene signature for significance in a data set as follows: 

library(limma)
geneSetTest(gene_sig, dataset)

where gene_sig is a vector of indices representing the genes in your gene group that match genes in your data set, and dataset is your healthy/disease data ordered by some statistic (i.e. ratio or p-value).

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written by seidel seidel

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