After statistical analysis (t-test/anova) on microarray data for differential gene expression with respect to a control, I finally have a list with the following information. Gene name , p-value, log fold change.
What i want to do now is to perform a Gene Set Expression Analysis with R. A book that I'm reading says that the first step is to create these gene sets by using Gene Ontology, KEGG or other databases and then run statistics (MLP/KS) to figure out which of these sets are enriched.
My question is how to do this very first step of creating the Gene Sets by having the data I previously mentioned (Gene name , p-value, log fold change). Is there any package function in R that is capable of doing such set unification ?