GSE

1. summary Gene set enrichment 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`