Question: Need your help to check MsigDB (it takes less than a minute)
gravatar for Na Sed
3.3 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 ""
Error: 'getBroadSets' failed to create gene sets:
  1: Unknown IO error2: failed to load external entity ""

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

broadset <- getBroadSets(asBroadUri('BIOCARTA_HDAC_PATHWAY'))
gsebase msigdb • 1.2k views
ADD COMMENTlink modified 3.1 years ago by Biostar ♦♦ 20 • written 3.3 years ago by Na Sed280
gravatar for Pierre Lindenbaum
3.3 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum126k wrote:

try: instead of

ADD COMMENTlink written 3.3 years ago by Pierre Lindenbaum126k

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

ADD REPLYlink written 3.3 years ago by Na Sed280

I just found it. The broadset <- getBroadSets(asBroadUri('BIOCARTA_HDAC_PATHWAY', base='')) works now!! Thank you very much!!

ADD REPLYlink written 3.3 years ago by Na Sed280
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