[BioC] Pathview - Problem with PNG output

[Christian De Santis]

Hi everyone,

I am running a KEGG analysis using Pathview to visualize my results. Everything works fine. However, for one of my pathway (01040 - Fatty Acid Biosynthesis), it fails to associate the values to the graph so that the png output does not show the genes that are up/down regulated. The code I run is the following:

pv.out.03050 <- pathview(gene.data = KO.BPC.fit.gd [,4], pathway.id = "03050", species = "ko", out.suffix = "BPC.proteasome", kegg.native = T)
pv.out.01040 <- pathview(gene.data = KO.BPC.fit.gd [,4], pathway.id = "01040", species = "ko", out.suffix = "BPC.FA.BIOS", kegg.native = T)

but I think it Is irrelevant since the first code, which is exactly the same as the second, works fine. Does anyone have any clue what the problem could be?

Also, for both codes I get the following warning message (although it does not seem to affect the output of the first code):

> pv.out.03050 <- pathview(gene.data = KO.BPC.fit.gd [,4], pathway.id = "03050", species = "ko", out.suffix = "BPC.proteasome", kegg.native = T)
[1] "Downloading xml files for ko03050, 1/1 pathways.."
[1] "Downloading png files for ko03050, 1/1 pathways.."
Working in directory H:/My Documents/R_Analyses/TSB/Screening
Writing image file ko03050.BPC.proteasome.png
Warning message:
In download.file(xml.url, xml.target, quiet = T) :
  downloaded length 14985 != reported length 200

Any help would be kindly appreciated,
Best Regards,
Christian

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