[BioC] Can gage not use large gene sets for pathway analysis?

Richard [guest] guest at bioconductor.org
Wed Dec 4 16:28:01 CET 2013

Hi Weijun Luo,
Using your two packages of gage and pathview, I have finished pathway analysis of signal transduction and identified two disturbed pathways from 40 pathways. But I met problem with metabolism pathway analysis, because I could not find any disturbed pathway with the metabolism gene sets (82 pathways) from Kegg. More weird, If I used whole gene sets for honeybees from kegg including the met/sig gene sets 122 pathways, the two disturbed signal pathways could not be find too. Some guys told me that this resulted from more gene sets, which increase p. values of each gene set. Is it true, and how can I solve this problem?
Thanks a lot!!

 -- output of sessionInfo(): 

XML Parsing Error: no element found
Location: file:///home/wenfu/CAseqanalysis/ameNA.xml
Line Number 2, Column 1:

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