rrvgo::calculateSimMatrix() error
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Michelle • 0
@2baccaed
Last seen 2 days ago
United States

I am using rrvgo to reduce the abundance of my GO terms table (tmp below). I ran this code previously, and it worked fine. However, it gave me this error below when I re-ran it recently. I have already subset it to only BP GO terms. Any suggestion will be much appreciated. Thanks.

  simMX <- calculateSimMatrix(tmp$dataSetID,
                              orgdb="org.Hs.eg.db",
                              ont="BP",
                              method="Rel")
  scores <- setNames(-log10(tmp$FDR), tmp$dataSetID)

  rt <- reduceSimMatrix(simMX,
                        scores,
                        threshold=0.5,
                        orgdb="org.Hs.eg.db")

preparing gene to GO mapping data... preparing IC data... Error in calculateSimMatrix(tmp$dataSetID, orgdb = "org.Hs.eg.db", ont = "BP", : (converted from warning) Removed 1 terms that were not found in orgdb for BP

rrvgo • 61 views
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Thanks for sharing the solution. It helps me. nced cloud

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