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• Maxime T. (admin)

[Maxime T.]

GSEAlite implements the Gene Set Enrichment Analysis. The leading edge plot, analysis of a list of gene sets and related statistics, i.e. enrichment scores, p-values, FDR and normalized enrichment scores.

This light version can reveal useful to quickly personalize figures and automatize the analysis in personal code.

The two main functions are:
GSEA.plot and GSEA.listofgenes

computeFDR and computeFDRmedian will give the FDR from the output of GSEA.listofgenes.

Usually gene set collections work with gene symbols or entrez id. It is thus needed to collapse rows when having multiple probes for one gene symbol. For that we usually use the max mean approach, i.e. we keep the probe set with maximal average expression across samples.

[Maxime T.]

Please note that this code is not perfect.

1st code Erratum:
in GSEA.plot function: NES was not computed adequately before Friday 27th February 2015. This is now improved.

NES computation will probably change again in the near future.