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Question

[Na Sed]

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'))

Answer 1

[Pierre Lindenbaum]

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

[Na Sed]

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

[Na Sed]

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!!