[BioC] annotation for illumina mouse-6 arrays? & GOstats

[Yupu Liang]

Hi,

Sorry for the long email,

I have two questions towards using GOstats for illumina mouse-6 data:

1-- I couldn't find the annotation package for illumina mouse-6 arrays  
under the downloads link,

Is there a way for me to generate it myself? I do have the annotation  
information for the platform?

2--I tried to generated the entrez list for all the genes from the  
chip through the following code -- ulist is list of gene symbol from  
the chip

x <- org.Mm.egSYMBOL2EG
mapped_genes <- mappedkeys(x)
xx <- as.list(x[mapped_genes])

ulist.entrez<-xx[ulist]
ulist.e <- unlist(glist.entrez,use.names=F)

The problem of my code is there was original 20183 symbols, after  
remove the duplications(multiple probes for one gene), I got 14430  
genes.
But only 244 of them have entrez ids -- which makes no GO term  
significant.

 > glist.entrez[1:5]

$`1110012J17Rik`
[1] "68617"

$<NA>
NULL

$`1110032E23Rik`
[1] "68659"

$<NA>
NULL

$<NA>
NULL


I am not sure what I did wrong? or how to get around this problem?

Thanks,
Yupu