[BioC] gene enrichment analysis without a control sample

Robert Castelo robert.castelo at upf.edu
Fri Nov 4 23:32:09 CET 2011

hi Wendy,

take a look at the GSVA package, it'll allow you to transform your 
gene-by-sample matrix of expression values into a gene-set-by-sample 
matrix of enrichment scores which can be interpreted as surrogates of 
expression level per gene set. take a look at the vignette, i think your 
situation might be similar to what is described in section 4.2 of the 


On 11/4/11 10:01 PM, Wendy Qiao wrote:
> Hi all,
> I have a microarray dataset compiled from several sources, so I am facing
> some challenges with identifying the expressed genes of each cell type. I
> am thinking to use the enriched gene sets of each cell type as the
> expressed genes of that cell type. However, the gene set enrichment
> analysis (http://www.broadinstitute.org/gsea/index.jsp) needs both control
> and sample data. I am wondering if there is gene set enrichment tool for
> the analysis of one cell type only.
> Thank you, Wendy
> 	[[alternative HTML version deleted]]
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