[BioC] gene enrichment analysis without a control sample

Wu, Di dwu at fas.harvard.edu
Fri Nov 4 22:21:57 CET 2011

Hi Wendy,

I am not sure whether using a right gene set test is your current problem. It seems you want to find the signature genes for each of the cell types.  Therefore, for this question, it seems a differential expression problem to me. 

I understand, when you have data from several cell types, you probably don't have one particular cell type as a control group to all other cell types. I had the similar problem in the mammary gland cell type data (Lim 2010, Nature Medicine). What I have done is to compare the cell type A to each of the other three cell types, then get the overlapped up (or down) regulated genes in the three comparisons. These genes are the signature genes (expressed genes or lower-expressed genes) for the cell type A. The same thing can be done for the other cell types. 

Regarding gene set tests,  testing which pathways, GO terms or other gene lists are enriched in your gene list,  there are different ways. Some required the raw data (our "roast" and "romer" functions in limma among others ). The geneSetTest function in limma only used the ranks of genes.

I will be happy to discuss with you more about gene set tests if that is actually what you face to or if you need to use them later. 

Hope this help,

Di Wu
Postdoctoral fellow
Harvard University, Statistics Department
Harvard Medical School
Science Center, 1 Oxford Street, Cambridge, MA 02138-2901 USA

From: bioconductor-bounces at r-project.org [bioconductor-bounces at r-project.org] On Behalf Of Wendy Qiao [wendy2.qiao at gmail.com]
Sent: Friday, November 04, 2011 5:01 PM
To: bioconductor at r-project.org
Subject: [BioC] gene enrichment analysis without a control sample

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

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