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作者 主題: [Tool] GAGE  (閱讀 1277 次)

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[Tool] GAGE
« 於: 四月 11, 2017, 05:15:41 pm »
https://pathview.uncc.edu/gageIndex

GAGE is an established method for gene set (enrichment or GSEA) or pathway analysis. GAGE is generally applicable to different omics data with robust performance.
 Quick Start
GAGE Web provides easy interactive access to GAGE analysis. It features:
A complete pathway analysis workflow based on GAGE and Pathview
Support to >3000 species, dozens of molecular IDs, various omics data and gene-set data (KEGG pathways, Gene Ontology, SMPDB etc);
Over-representation test on preselected gene or molecule lists.
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回覆: [Tool] GAGE
« 回覆文章 #1 於: 四月 15, 2017, 11:05:48 am »
https://rdrr.io/bioc/gage/man/gage.html

Test signficance or statistics columns include:

p.geomean   
geometric mean of the individual p-values from multiple single array based gene set tests
stat.mean   
mean of the individual statistics from multiple single array based gene set tests. Normally, its absoluate value measures the magnitude of gene-set level changes, and its sign indicates direction of the changes. When saaTest=gs.KSTest, stat.mean is always positive.
p.val   
gloal p-value or summary of the individual p-values from multiple single array based gene set tests. This is the default p-value being used.
q.val   
FDR q-value adjustment of the global p-value using the Benjamini & Hochberg procedure implemented in multtest package. This is the default q-value being used.
set.size   
the effective gene set size, i.e. the number of genes included in the gene set test
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