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

[Marc Carlson]

Hi Yupu,

To learn how to make a custom package, please see the SQLForge vignette
in the AnnotationDbi package.  You can find it here:

http://www.bioconductor.org/packages/devel/bioc/html/AnnotationDbi.html


  Marc


Yupu Liang wrote:
> 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
>
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