9 Gene set analysis in iRAP

Gene set enrichment analysis in iRAP

iRAP can perform gene set enrichment (GSE) analysis based on the differential expression results. Currently only the http://www.bioconductor.org/packages/release/bioc/html/piano.html Piano tool is supported but the following methods available in Piano may be used: mean, median, sum, fisher, stouffer, tailStrength, wilcoxon, reporter, and page. For information about these methods and Piano we refer to the Piano documentation available http://www.bioconductor.org/packages/release/bioc/html/piano.html here.

To enable GSE analysis in iRAP is necessary to explicitly enable it in the configuration file by defining the tool that is going to perform the analysis.

`gse_tool=piano`

The GSE method can be defined using the gse_method variable. For instance, to use a Fisher test (default test) one should include the following line in the configuration file.

`gse_method=fisher`

The minimum number of genes that a set must is defined using the gse_minsize variable. For instance, to define the minimum number of genes to 4 one would include the following line in the configuration file.

`gse_minsize=4`

The p-value cut-off can be defined using the gse_pvalue variable.

`gse_pvalue=0.05`