[BioC] problem with lumiRatAll.db

[Flora Fan]

Hi,

I am trying to use lumi package to analyze Illumina RatRef-12_V1. 
However, about 30% of the probe IDs don't have annotations in 
lumiRatAll.db_1.6.1. Is it because the mapping didn't pass the threshold 
or am I doing something wrong?

For example, for probe ID ILMN_1355285:
nuID = Niuq09_43JW4K1SOe4
probe seq = GAGGTGGGGTCATTCTTGTGATCTAGCCCGTGAAGGTCCCAGATGCTGTG
manual blast result as well as Illumina annotation file 
RatRef-12_V1_0_R3_11222119_A.txt shows that it mapped to A4galt.

But when I do getSYMBOL, no symbol was returned.
 > getSYMBOL("Niuq09_43JW4K1SOe4","lumiRatAll.db")
Niuq09_43JW4K1SOe4
                NA
or
 >  x<- lumiRatAllACCNUM
 >  mapped_probes <- mappedkeys(x)
 >  ind<-c(1:16134)[mapped_probes == "Niuq09_43JW4K1SOe4"]
It returned integer(0)

How can I annotate these IDs? Can I keep the original gene symbols that 
were generated from GenomeStudio version 1.0.6 as identifiers in lumi 
package?

Here is the sessionInfo()
R version 2.9.1 (2009-06-26)
i386-apple-darwin8.11.1

locale:
en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base    

other attached packages:
 [1] lumiRatAll.db_1.6.1    lumiRatV1_1.2.0        beadarray_1.12.1     
 [4] hwriter_1.1            lumiRatIDMapping_1.2.1 limma_2.18.0         
 [7] lumi_1.10.2            RSQLite_0.7-1          DBI_0.2-4            
[10] preprocessCore_1.6.0   mgcv_1.5-5             affy_1.22.0          
[13] annotate_1.22.0        AnnotationDbi_1.6.0    Biobase_2.4.1        

loaded via a namespace (and not attached):
[1] affyio_1.12.0   grid_2.9.1      lattice_0.17-25 nlme_3.1-92   
[5] tools_2.9.1     xtable_1.5-5  

Your help will be greatly appreciated.
-Flora

-- 
Flora 
Biostatistics and Informatics
Masonic Cancer Center, University of Minnesota