Hi there,

I hope someone of you can help me with this, i couldn't find anything online. I tried to map chicken orthologues from a list of human ENSEMBLPROT ids using package "hom.Hs.inp.db":

str(ids)

 chr [1:319] "ENSP00000469853" "ENSP00000472959" "ENSP00000469805" ...

chickIDs <- select (org.Hs.eg.db, keys= ids, columns= "ENSEMBLPROT",keytype= "ENTREZID")

Unfortunately i get the following warning:

Warning message:

In `[<-.factor`(`*tmp*`, iseq, value = c("ENSP00000469853", "ENSP00000472959",  :

  invalid factor level, NA generated

So, i do get some orthologues, however the majority of rows were replaced with NAs from human ENSEMBLPROT ids so i guess something wrong happened?

head(chickIDs)

     HOMO_SAPIENS      GALLUS_GALLUS

1 ENSP00000304096 ENSGALP00000005396

2 ENSP00000300013               <NA>

3 ENSP00000368814               <NA>

4 ENSP00000304360 ENSGALP00000004786

5 ENSP00000296277               <NA>

6 ENSP00000360382 ENSGALP00000017466

tail(chickIDs)

    HOMO_SAPIENS GALLUS_GALLUS

314         <NA>          <NA>

315         <NA>          <NA>

316         <NA>          <NA>

317         <NA>          <NA>

318         <NA>          <NA>

319         <NA>          <NA>

Thanks a lot in advance! 

 sessionInfo()

R version 3.2.0 (2015-04-16)

Platform: x86_64-apple-darwin13.4.0 (64-bit)

Running under: OS X 10.10.3 (Yosemite)

locale:

[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:

[1] parallel  stats4    stats     graphics  grDevices utils     datasets 

[8] methods   base     

other attached packages:

 [1] org.Hs.eg.db_3.1.2   hom.Hs.inp.db_3.1.2  org.Gg.eg.db_3.1.2  

 [4] RSQLite_1.0.0        DBI_0.3.1            AnnotationDbi_1.30.1

 [7] GenomeInfoDb_1.4.0   IRanges_2.2.1        S4Vectors_0.6.0     

[10] Biobase_2.28.0       BiocGenerics_0.14.0  BiocInstaller_1.18.4

loaded via a namespace (and not attached):

[1] tools_3.2.0