Sudden error with KEGG analysis using gometh
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pedro-marra ▴ 10
@1025d521
Last seen 1 day ago
United States

I have generated KEGG tables from a differential methylation table many times before with the following code

annoEPIC <- getAnnotation(IlluminaHumanMethylationEPICanno.ilm10b4.hg19)

tablep0.005 <- diffMethTable0.05[1:186,]
sig.cpg0.005 <- as.character(tablep0.005[,2])

kegg <- gometh(sig.cpg = sig.cpg0.005, all.cpg = NULL, collection = "KEGG", array.type = "EPIC",
plot.bias = TRUE)


However, during this past week I have been getting this error message, which I had never gotten before:

Error in file(file, "rt") : cannot open the connection
In file(file, "rt") :
cannot open URL 'http://rest.kegg.jp/list/pathway/Hsa': HTTP status was '400 Bad Request'
sessionInfo( )


When I paste the URL that the error message mentions on Google, the page does not load. However, when I use the URL: https://rest.kegg.jp/list/pathway/hsa it does!

Has anyone else running gometh (with KEGG) been getting this message as well? How would I make gometh use the correct URL then?

I appreciate any help.

KEGG gometh • 168 views
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I am having the exact same problem. Any ideas anyone please?

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I'm having the same issue. Not sure whats going on either.

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@james-w-macdonald-5106
Last seen 5 hours ago
United States

This has been fixed in both release and devel. It will take a day or two to propagate to the download servers, at which time you can update using BiocManager.

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Thank you very much! Now it is working!