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Old 03-21-2014, 03:37 AM   #47
shriram
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Location: UK

Join Date: May 2010
Posts: 13
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pv.out.list <- sapply(enriched_pathways, function(pid) pathview(gene.data = gene_fc, pathway.id = pid, species = "sce", gene.idtype="KEGG", same.layer = F, kegg.native = T, node.sum="median"))

Data in pathview:
pv.out.list[1]
GLK1 -0.35 0.000 0.620 -1.118 -0.900

# original data supplied for pathview
gene_fc[1,]
GLK 0.14 -1.6 0.62 -1.1 -0.37

I have attached the resultant pathway image.
Original image sce00051.png shows genes specific[in green] to yeast.

I am wondering why pathview data differ for GLK when GLK is the only gene on that node.

Thanks,
Shriram
Attached Images
File Type: png sce00051.Fructose_and_mannose_metabolism_.multi.png (28.3 KB, 9 views)
File Type: png sce00051.png (33.4 KB, 2 views)
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