Question

Sudden error with KEGG analysis using gometh

1

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pedro-marra ▴ 10

@1025d521

Last seen 20 months 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)
diffMethTable0.05 <- read.csv("diffMethTable_site_cmp9_0.05.csv", header = TRUE)

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 addition: Warning message:
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 • 3.7k views

ADD COMMENT • link updated 18 months ago by Aung • 0 • written 21 months ago by pedro-marra ▴ 10

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I am having the exact same problem. Any ideas anyone please?

ADD REPLY • link 21 months ago rkyhung ▴ 20

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

ADD REPLY • link 20 months ago anmolanp ▴ 10

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I updated the packages that generate the KEGG tables (and also GO tables) and the tables were really different from what I had previously gotten with the other package version. Is this expected?

ADD REPLY • link 20 months ago pedro-marra ▴ 10

score 0 · Answer 1 · 2023-03-16

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 3 days 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.

ADD COMMENT • link 20 months ago James W. MacDonald 67k

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Thank you very much! Now it is working!

ADD REPLY • link 20 months ago pedro-marra ▴ 10

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I updated the packages that generate the KEGG tables (and also GO tables) and the tables were really different from what I had previously gotten with the other package version. Is this expected?

ADD REPLY • link 20 months ago pedro-marra ▴ 10

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For KEGG, yes. You previously couldn't get results, and now you can, so by definition I would expect differences. As for GO, the only change I made was to change Hsa to hsa in the URI for KEGG, so I would not expect any differences for GO due to any changes I made.

It would also be helpful if you provided a self-contained example that others can run to see what you are talking about. Simply saying the tables are different is not much to go on.

ADD REPLY • link 20 months ago James W. MacDonald 67k

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Thank you very much! I installed two packages that R kept saying that needed to be installed, and now I am getting the same results as before!

ADD REPLY • link 20 months ago pedro-marra ▴ 10

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Hi James,

I currently have the same problems. When I install missMethyl and I run the following code KEGG <- gometh(sig.cpg, all.cpg = all.cpg, collection = c("KEGG"), array.type = c("EPIC"), plot.bias = TRUE, prior.prob = TRUE)

I get the error message as follow: Error in file(file, "rt") : cannot open the connection In addition: Warning message: In file(file, "rt") : cannot open URL 'http://rest.kegg.jp/list/pathway/Hsa': HTTP status was '400 Bad Request'

Please let me know how I can solve this problem. Last February, I ran the similar analysis and I get the results table.

Thanks in advance.

ADD REPLY • link 18 months ago Aung • 0

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I assume you are using an old version of R/Bioc, in which case you need to upgrade.