Hi bigmw,
With your kind help, I have finished pathway analysis of signal transduction and fond two disturbed pathways. But I met problem with metabolism pathway analysis, because I could not find any disturbed pathway with the metabolism gene sets from Kegg. More weird, If I used whole gene sets for honeybees from kegg including the met/sig gene sets, 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. Do you have any idea on this strange problem?
Thanks a lot!!
Richard
With your kind help, I have finished pathway analysis of signal transduction and fond two disturbed pathways. But I met problem with metabolism pathway analysis, because I could not find any disturbed pathway with the metabolism gene sets from Kegg. More weird, If I used whole gene sets for honeybees from kegg including the met/sig gene sets, 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. Do you have any idea on this strange problem?
Thanks a lot!!
Richard
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