Question

UnProducible error with goana and kegga function

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Ahdee ▴ 50

@ahdee-8938

Last seen 12 weeks ago

United States

Hi so I been running many scripts without an issue for both goana and kegga, however just today, the same script with the same input is giving this error.

Error in read.table(URL, sep = "\t", quote = "\"", fill = TRUE, comment.char = "",  : 
  duplicate 'row.names' are not allowed

My generic code is something like this.

 kegga(list(Up=up, Down=down),
                  species="Hs",
                  universe=bg, FDR=.05)

where down and up are gene vectors. I even check to see if up and down are unique which they are. Does anyone else have the same issue or know the solution?

A related question is that on the document it says that " one can supply the required pathway annotation to kegga in the form of two data.frames" does anyone know how I can download and supply this locally?

many thanks in advance!

edit: upon looking at this closely I think this is due to kegg server being down. For example looking at the source code I believe this is were the error is: http://rest.kegg.jp/link/pathway/Hs and df = getGeneKEGGLinks () gives the same error msg!

limma goana kegga • 1.4k views

ADD COMMENT • link updated 5.1 years ago by Gordon Smyth 51k • written 5.1 years ago by Ahdee ▴ 50

score 0 · Answer 1 · 2019-09-23

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Gordon Smyth 51k

@gordon-smyth

Last seen 4 hours ago

WEHI, Melbourne, Australia

limma::getGeneKEGGLinks() works correctly for me.

The KEGG server isn't down. The URL you give is not actually a correct KEGG URL. The reason it doesn't work is that you've inserted a Bioconductor style species name where as KEGG style name is needed.

To be honest, I don't see how the error you report could have arisen from any of the limma functions. The error message implies a read.table call that specifies a row.names column, but none of the limma functions do that.

Whatever the cause, the problem would seem to be at your end because, as you say, it just started today with no change in the limma code. If you want to take the question further, you would need to give the complete code that leads to the error message.

ADD COMMENT • link 5.1 years ago Gordon Smyth 51k

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Thanks Gordon: I don't know why but it seem to be working again. And the same function used yesterday df = getGeneKEGGLinks () seem to be working again. May be it just so happen that the server was back up when you tried it? I don't know but glad its working again. I'm going to store this locally just in case. Thanks.

ADD REPLY • link 5.1 years ago Ahdee ▴ 50

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No, the KEGG server couldn't have been down. The error message in that case would have been completely different. The error message in that case would have said that the URL couldn't be found.

The error message you report says that a data.frame has been read but the specified row names are not correct. To get this error message you must (1) specify headers or row names in the read.table call and (2) successfully read at least two rows of data. But (1) is not done by the limma code and (2) couldn't occur if the server was down.

According to my knowledge of the R language, the error message you reported cannot arise in any circumstances from limma::getGeneKEGGLinks().

ADD REPLY • link 5.1 years ago Gordon Smyth 51k