[BioC] equiry about GAGE

Luo Weijun luo_weijun at yahoo.com
Tue Dec 7 02:57:14 CET 2010

Hi Jingqin,
Thanks for the comments and interest!
We do provide some decent utilities in the gage package for Result Presentation and Intepretation. Please check section 5 of the vignette for details. Specifically for your question, we can extract core genes and visualize their expression data with essGene and geneData functions. Please check their help info for details. We may even do multiple parallel analyses in a batch, and compare their results using some pipeline routines in the package. Again, please check the the vignette for details.
I used GSEA quite a while ago. I am not that familiar with the output from its recent versions. If you want some html/webpage type of output, gage package don’t do that at this time. But we may consider adding it later if there is enough interest in doing this. Thanks!

On 12/6/2010 7:15 PM, wu jingqin wrote:
> Hi Luo WenJun,
> I just tried your GAGE package on my mRNA sequencing data.
> The output files make sense and the speed is fast. Great work.
> But one thing might be a pity.
> Previously I used GSEA and the output has more information for each gene 
> set.
> For example, you can click on each gene set enriched and looked at the 
> list of genes with core enrichment genes highlighted. In addition, it 
> provides a heat map between 2 groups for each gene in that gene set.
> Just wondering will it be possible to get GSEA-like output from your 
> package?
> How to do it?
> Looking forward to your reply
> Cheers
> Jingqin Wu
> School of Biomedical Sciences
> University of Newcastle

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