[BioC] Annotation databases--unable to get annotations

[James W. MacDonald]

Hi Manjula,

On 10/10/2012 2:31 PM, Manjula Kasoji [guest] wrote:
> Has anyone used the mogene10stprobeset.db annotation package?
>
> I have a list of significant probeset ids that I obtained from running an analysis in the limma package. When I try to use mget() to retrieve the corresponding gene names only a couple of probesets get annotated. I've tried with several different gene lists. In a gene list of about 300 genes, only 2 get annotated at the most. The rest of the probesets get a "NA" for the annotation.
>
> Here is my R code:

That's not all your code, just some. You might also note that you used 
the affy package to summarize, in which case you have summarized at the 
transcript level, not the probeset level. So you are using the wrong 
annotation package. Try the mogene10sttranscriptcluster.db package and 
see how that works.

Best,

Jim


>
> ## load library
>> library("mogene10stprobeset.db")
> ## map probe ids to gene names...
>
> #extract ids from signifcant gene list
> ids=sig.gene.list[["ID"]]
>
> #if not in character form, change to character
> ids = as.character(ids)
>
> #retrieve gene names from annotation package for ids in signficant gene list
> mget(ids, mogene10stprobesetGENENAME, ifnotfound=NA)
>
>
> I've tried ENTREZID, SYMBOL, and GO, all of them return annotations just for a few probesets.
>
> I'm using R version R 2.15.1 for Macs.
>
> Any help would be appreciated!!
>
> Thanks!
>
>   -- output of sessionInfo():
>
>> sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>   [1] hgu95av2.db_2.7.1           org.Hs.eg.db_2.8.0          limma_3.14.0                mogene10stv1cdf_2.11.0      affy_1.36.0                 mogene10stprobeset.db_8.0.1 org.Mm.eg.db_2.8.0
>   [8] RSQLite_0.11.2              DBI_0.2-5                   AnnotationDbi_1.20.0        Biobase_2.18.0              BiocGenerics_0.4.0          BiocInstaller_1.8.2
>
> loaded via a namespace (and not attached):
> [1] affyio_1.26.0         IRanges_1.16.2        parallel_2.15.1       preprocessCore_1.20.0 stats4_2.15.1         tools_2.15.1          zlibbioc_1.4.0
> --
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>
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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