Warning message as converting gene Symbol to ENTREZID
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@do-it-23093
Last seen 1 day ago
Germany, München

Hello Dears,

Could please advise me on how to solve some of the genes that bitr() function fail to convert gene SYMBOL TO ENTREZID. This is the command line that I used in clusterprofiler package

sig.gene <- bitr(rownames(gene),
fromType="SYMBOL",
toType = "ENTREZID",
OrgDb = org.Hs.eg.db)


here is the warning message.

In bitr(rownames(gene), fromType = "SYMBOL", toType = "ENTREZID",  :
9.61% of input gene IDs are fail to map...


Thank you so much for your help!!!

go clusterprofiler • 1.3k views
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@james-w-macdonald-5106
Last seen 2 days ago
United States

Some of your symbols might have been deprecated, in which case they are now an alias. So you might try using fromType = "ALIAS" to see if that helps. Otherwise it's not completely unexpected that a gene symbol might not map. Symbols are not necessarily unique, and sometimes what you have are not the official versions, so it can be difficult to get everything to map. If ~10% isn't that many, you could try finishing up by hand.