Hi all,

I am using clusterProfiler to perform KEGG enrichment. I have a list of gene Symbol (Rat genes). First I need to translate the symbols to EntrezID.

I installed the Genome wide annotation for Rat:

    source("https://bioconductor.org/biocLite.R")
    biocLite("org.Rn.eg.db")

Then I tried to run the command:

    x <- c("GPX3",  "GLRX",   "LBP",   "CRYAB", "DEFB1", "HCLS1",   "SOD2",   "HSPA2",
           "ORM1",  "IGFBP1", "PTHLH", "GPC3",  "IGFBP3","TOB1",    "MITF",   "NDRG1",
           "NR1H4", "FGFR3",  "PVR",   "IL6",   "PTPRM", "ERBB2",   "NID2",   "LAMB1",
           "COMP",  "PLS3",   "MCAM",  "SPP1",  "LAMC1", "COL4A2",  "COL4A1", "MYOC",
           "ANXA4", "TFPI2",  "CST6",  "SLPI",  "TIMP2", "CPM",     "GGT1",   "NNMT",
           "MAL",   "EEF1A2", "HGD",   "TCN2",  "CDA",   "PCCA",    "CRYM",   "PDXK",
           "STC1",  "WARS",  "HMOX1", "FXYD2", "RBP4",   "SLC6A12", "KDELR3", "ITM2B")

    eg = bitr(x, fromType="SYMBOL", toType="ENTREZID", OrgDb="org.Rn.eg.db")

Then I got the warning message:

> 'select()' returned 1:1 mapping between keys and columns Warning
> message: In bitr(x4, fromType = "SYMBOL", toType = "ENTREZID", OrgDb =
> Rat) :
>   98.21% of input gene IDs are fail to map...

Could anyone tell me what happened and how should I do?

Many thanks,
Stanley
```
> paste0(substring(x, 1, 1), tolower(substring(x, 2))) -> x2
> x2[x2=="Pvr"] = "PVR"
> eg = bitr(x2, fromType="SYMBOL", toType="ENTREZID", OrgDb="org.Rn.eg.db")
'select()' returned 1:1 mapping between keys and columns
> eg
    SYMBOL ENTREZID
1     Gpx3    64317
2     Glrx    64045
3      Lbp    29469
4    Cryab    25420
5    Defb1    83687
6    Hcls1   288077
7     Sod2    24787
8    Hspa2    60460
9     Orm1    24614
10  Igfbp1    25685
11   Pthlh    24695
12    Gpc3    25236
13  Igfbp3    24484
14    Tob1   170842
15    Mitf    25094
16   Ndrg1   299923
17   Nr1h4    60351
18   Fgfr3    84489
19     PVR    25066
20     Il6    24498
21   Ptprm    29616
22   Erbb2    24337
23    Nid2   302248
24   Lamb1   298941
25    Comp    25304
26    Pls3    81748
27    Mcam    78967
28    Spp1    25353
29   Lamc1   117036
30  Col4a2   306628
31  Col4a1   290905
32    Myoc    81523
33   Anxa4    79124
34   Tfpi2   286926
35    Cst6   171096
36    Slpi    84386
37   Timp2    29543
38     Cpm   314855
39    Ggt1   116568
40    Nnmt   300691
41     Mal    25263
42  Eef1a2    24799
43     Hgd   360719
44    Tcn2    64365
45     Cda   362638
46    Pcca   687008
47    Crym   117024
48    Pdxk    83578
49    Stc1    81801
50    Wars   314442
51   Hmox1    24451
52   Fxyd2    29639
53    Rbp4    25703
54 Slc6a12    50676
55  Kdelr3   315131
56   Itm2b   290364
```

I think we should raise this issue to Bioconductor. IMO, Mapping ID with case insensitive is necessity.
