annotation error

[Ellie Duan]

Hello,
I had an error when running detailRanges in csaw using fly genome:

library(TxDb.Dmelanogaster.UCSC.dm6.ensGene)
library(org.Dm.eg.db)
anno <- detailRanges(rowRanges(filtered.data), orgdb=org.Dm.eg.db,
                     txdb=TxDb.Dmelanogaster.UCSC.dm6.ensGene)

Here is the message:

Error in .testForValidKeys(x, keys, keytype, fks) : 
  None of the keys entered are valid keys for 'ENTREZID'. Please use the keys method to see a listing of valid arguments.

Any suggestions?

Thank you very much!

Best,
Ellie

[Aaron Lun]

I daresay that you need to fiddle with the key.field= and name.field= arguments. I assume that TxDb.Dmelanogaster.UCSC.dm6.ensGene uses ENSEMBL IDs as the keys, so perhaps key.field="ENSEMBL" would work.

[Ellie Duan]

Yes! Thank you for your help!