Question: Need your help to check MsigDB (it takes less than a minute)
0
gravatar for Na Sed
2.5 years ago by
Na Sed280
United States
Na Sed280 wrote:

In previous month I used to run the bellow code the gene sets from MSigDB database. But now I get an error.

Unknown IO errorfailed to load external entity "http://www.broad.mit.edu/gsea/msigdb/cards/BIOCARTA_HDAC_PATHWAY.xml"
Error: 'getBroadSets' failed to create gene sets:
  1: Unknown IO error2: failed to load external entity "http://www.broad.mit.edu/gsea/msigdb/cards/BIOCARTA_HDAC_PATHWAY.xml"

Could you please run the code on your system to see whether you get the error as I?

library(GSEABase)
broadset <- getBroadSets(asBroadUri('BIOCARTA_HDAC_PATHWAY'))
gsebase msigdb • 993 views
ADD COMMENTlink modified 2.2 years ago by Biostar ♦♦ 20 • written 2.5 years ago by Na Sed280
2
gravatar for Pierre Lindenbaum
2.5 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum119k wrote:

try: http://software.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_HDAC_PATHWAY.xml instead of http://www.broad.mit.edu/gsea/msigdb/cards/BIOCARTA_HDAC_PATHWAY.xml

ADD COMMENTlink written 2.5 years ago by Pierre Lindenbaum119k

Thanks. So, 'getBroadSets' does not work anymore?!

ADD REPLYlink written 2.5 years ago by Na Sed280

I just found it. The broadset <- getBroadSets(asBroadUri('BIOCARTA_HDAC_PATHWAY', base='http://software.broadinstitute.org/gsea/msigdb/cards')) works now!! Thank you very much!!

ADD REPLYlink written 2.5 years ago by Na Sed280
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