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Old 03-18-2014, 06:58 PM   #39
bigmw
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Join Date: Aug 2013
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If you are look for the gene entry"120" underpv.out.list[[1]]$plot.data.gene, it may or may not be different from the original data, cnts.d, because multiple genes may be mapped to the same nodes in a KEGG pathway. What you found in $plot.data.gene is the node level summary instead of single gene data. Each node there is labeled or named after the most representative member gene.

Please check the pathview tutorial (page 7) and documentations for more details:
http://bioconductor.org/packages/rel.../pathview.html
http://bioconductor.org/packages/rel...c/pathview.pdf
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