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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
Thanks for sharing the solution. It helps me. nced cloud