I have generated an excel spreadsheet using DESEQ2 and trying to convert bacterial (Streptococcus gordonii) geneIDs to gene names.
> readfile$symbol<-mapIds(org.Hs.eg.db, keys = row.names(readfile), keytype = "ENSEMBL", column = "SYMBOL")
Error in .testForValidKeys(x, keys, keytype, fks) :
None of the keys entered are valid keys for 'ENSEMBL'. Please use the keys method to see a listing of valid arguments.
This is what my geneIDs look like:
SGO_0387
SGO_0749
SGO_0955
SGO_2105
SGO_0524
SGO_2076
SGO_0522
SGO_0217
SGO_0267
SGO_0711
SGO_0561
I assume that I am using the wrong database, but I do not understand where those IDs belong to as they appear on ENSEMBL, NCBI and Uniprot.
org.Hs.eg.db database is for human (see org.Hs.eg.db), no wonder why the bacterial IDs are not mapping :). You would have to find the equivalent for your species, or maybe use other method for the ID conversion.
Thank you!
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