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!
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.
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