search

Oshlack / missMethyl

Bioconductor package for analysis of methylation data from Illumina's Infinium HumanMethylation arrays.
10 stars 4 forks source link

Calling gometh(sig.cpg, collection = 'KEGG') results in error, cannot open URL #18

Closed sbasrai98 closed 1 year ago

sbasrai98 commented 1 year ago

Hello,

I'm running into the following problem when trying to call gometh for KEGG pathway enrichment:

> kegg.result = gometh(sig.cpg = sms, collection = 'KEGG')
All input CpGs are used for testing.
Error in file(file, "rt") : 
  cannot open the connection to 'http://rest.kegg.jp/list/pathway/Hsa'
In addition: Warning message:
In file(file, "rt") :
  cannot open URL 'https://rest.kegg.jp/list/pathway/Hsa': HTTP status was '400 Bad Request'

Trying to paste the URL into my browser does indeed lead to an HTTP 400 error. The URL works when "Hsa" is instead "hsa". Do you know how I can fix this/change the URL gometh tries to connect to?

Thanks, SB

bphipson commented 1 year ago

We have fixed this bug, please reinstall the limma and missMethyl packages.

Thanks!