Need your help to check MsigDB (it takes less than a minute)
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'))
1 answer
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
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Pierre Lindenbaum
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!!
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