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Posts by yingchen
... Hi Monther, Thanks a lot for the explanation! I have another question, what is the recommended cut-off for significant DE gene sets and pathways? When I used GAGE for the same data set, in 1 contrast, there are only 13 kegg pathways with q.val <= 0.01. When I did the analysis with EGSEA, the q. ...
EGSEA: how does the program generate the value for the up or down regulation of gene sets or pathways
... Hi guys, I tried the EGSEA package and was hoping to find a better way to do the GSEA. The output column Direction under gsa$mylabel$test.results$mycontrast gives values 1,0, -1. I assume that -1 means the gene set/pathway is down-regulated and 1 means it's up-regulated. My problem is that most of ...
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