In trying to re-run my pathway analysis with a DEG set annotated with gene symbols. I have encountered this error while wanting to retrieve Entrez IDs for clusterProfiler. This is a new error, as I have worked with the same script before.
up.genes.entrez <- clusterProfiler::bitr(up.genes,fromType = "SYMBOL",toType = "ENTREZID",OrgDb = org.Hs.eg.db) Error in .testForValidKeys(x, keys, keytype, fks) : None of the keys entered are valid keys for 'SYMBOL'. Please use the keys method to see a listing of valid arguments.
I can not figure out why keytype SYMBOL are not recognized as valid gene symbols anymore. I have tried reinstalling or updating the packages and I would be most grateful for additional suggestions.
Can you look at your
dbfile? Sometimes symbol is hgnc_symbol.
Please share a reproducible example, we need to know what is