[BioC] Creating Annotation package for GPL10427

[James W. MacDonald]

Hi Kaj,

Currently you cannot create a chip level annotation package without a 
corresponding .db0 package. You can however create an organism level 
package using makeOrgPackageFromNCBI() in the AnnotationForge package, 
and then getting the annotation file from Agilent. You can then use the 
Entrez Gene IDs from the annotation file to then use select() to get 
whatever annotation you might want.

If you are using limma, you can put the annotation data in the genes 
slot of the MArrayLM object, and those data will appear in your 
topTables().

Best,

Jim



On Thursday, October 03, 2013 6:21:22 AM, Kaj Chokeshaiusaha [guest] 
wrote:
>
> Dear R helper,
>
> I'm trying to create the annotation package for GPL10427. It is ovine species platform, and there is no .db0
> nor schema for it.
>
> I'm trying to read 'Creating an annotation package
> with a new database schema'. It's ashamed of me, but I'm an R beginner. I must accept that I loss most of the
> important contents and I cannot gather enough ideas to apply it with what I have to do.
>
> Would anyone please simplify me what I need to do in order to create the platform in this situation?
>
> With Respects,
> Kaj
>
>   -- output of sessionInfo():
>
> R version 3.0.2 (2013-09-25)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
>   [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
>   [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
>   [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8
>   [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
>   [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats     graphics  grDevices utils     datasets  methods
> [8] base
>
> other attached packages:
> [1] hgu95av2.db_2.9.0     AnnotationForge_1.2.2 org.Hs.eg.db_2.9.0
> [4] RSQLite_0.11.4        DBI_0.2-7             AnnotationDbi_1.22.6
> [7] Biobase_2.20.1        BiocGenerics_0.6.0
>
> loaded via a namespace (and not attached):
> [1] IRanges_1.18.4 stats4_3.0.2   tcltk_3.0.2    tools_3.0.2
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099