[BioC] Oligo package annotation

[James W. MacDonald]

On 12/13/2012 11:48 AM, Bruno [guest] wrote:
> Hi all,
> My question is quite straight-forward: how do i retrieve EntrezId or geneSymbol for pd.hugene.1.1.st.v1 to merge into my gene expression matrix? I havent found any vignettes explaining this. I know that the annotation file is a SQLite DB which i have to query. However im failing to find the tables i need. Sorry if i persevere in not explaining myself enough.

It depends on what level you used for summarization. Assuming that you 
used transcript-level summarization (which I would highly recommend), 
you want to use the hugene11sttranscriptcluster.db package. If you did 
something like

rma(<filename>, target="probeset")

then you want the hugene11stprobeset.db

Best,

Jim


>
>
>   -- output of sessionInfo():
>
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
> [4] LC_NUMERIC=C                            LC_TIME=English_United Kingdom.1252
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>   [1] pd.hugene.1.1.st.v1_3.8.0 oligo_1.22.0              affyPLM_1.34.0            preprocessCore_1.20.0     latticeExtra_0.6-24
>   [6] lattice_0.20-10           RColorBrewer_1.0-5        BiocInstaller_1.8.3       simpleaffy_2.34.0         gcrma_2.30.0
> [11] genefilter_1.40.0         affy_1.36.0               limma_3.14.3              RSQLite_0.11.2            DBI_0.2-5
> [16] Biobase_2.18.0            oligoClasses_1.20.0       BiocGenerics_0.4.0
>
> loaded via a namespace (and not attached):
> Error in x[["Version"]] : subscript out of bounds
> In addition: Warning message:
> In FUN(c("affxparser", "affyio", "annotate", "AnnotationDbi", "Biostrings",  :
>    DESCRIPTION file of package 'survival' is missing or broken
>
> --
> 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