O'Reilly logo

Bioinformatics with R Cookbook by Paurush Praveen Sinha

Stay ahead with the world's most comprehensive technology and business learning platform.

With Safari, you learn the way you learn best. Get unlimited access to videos, live online training, learning paths, books, tutorials, and more.

Start Free Trial

No credit card required

The functional enrichment of data

Once we know the DE genes from our array data, we have all the genes that somehow play a role in the cell. In order to know more about this set of genes at a biological level, we need to know their biological role in terms of their function. Analyzing the GO categories in the set can do this. This recipe is about the enrichment of gene sets with GO terms.

Getting ready

The recipe explained here will require the gene set data that comes from our analysis and the annotation package indicated in the ExpressionSet object (hgu95av2.db).

How to do it…

Perform the following steps to describe the enrichment of genes with GO terms via a hypergeometric test:

  1. First, install and load the annotation database and GOstats library ...

With Safari, you learn the way you learn best. Get unlimited access to videos, live online training, learning paths, books, interactive tutorials, and more.

Start Free Trial

No credit card required