[BioC] mogene10stv1 annotation problem

[James W. MacDonald]

Hi Dave,

If you are using the mogene10stv1cdf to compute expression values, then 
by default you are using the transcript clusters rather than the 
probesets. You therefore want the mogene10sttranscriptcluster.db package.

 > length(ls(mogene10stv1cdf))
[1] 34760
 > sum(ls(mogene10stv1cdf) %in% Lkeys(mogene10sttranscriptclusterENTREZID))
[1] 34728
 > sum(ls(mogene10stv1cdf) %in% Lkeys(mogene10stprobesetENTREZID))
[1] 6658

Best,

Jim



Dave Crawford wrote:
> Many thanks for your prompt reply Vincent!
> 
> Initially, it looked trivial and it did work, but!...
> How can my ExpressionSet from 34760 features go down to 85? It can't be possible that in that chip there are only 85 probe sets with Entrez ID, or?
> 
> Dave
> 
> 
> Date: Mon, 31 May 2010 02:28:40 -0400
> Subject: Re: [BioC] mogene10stv1 annotation problem
> From: stvjc at channing.harvard.edu
> To: arhaios50 at hotmail.com
> CC: bioconductor at stat.math.ethz.ch
> 
> because you have set require.entrez=TRUE, some mapping package must be used to check for entrez ids that correspond to the featureName elements of your ExpressionSet.  annotation(vsnrmadata) evaluates to "mogene10stv1", and AFAIK there is no bioconductor annotation package with that name (although you could make one if you wanted to).  Because your sessionInfo suggests that mogene10stprobeset.db_5.0.1 is a mapping that you are interested in, you could probably do
> 
> 
> annotation(vsnrmadata) = "mogene10stprobeset.db"
> 
> and get better results with your nsFilter call.
> 
> On Sun, May 30, 2010 at 1:59 PM, Dave Crawford <arhaios50 at hotmail.com> wrote:
> 
> 
> 
> Dear list,
> 
> 
> 
> I am trying the following and I am getting an error. Could you help me please?
> 
> 
> 
> Thanks!
> 
> Dave
> 
> 
> 
>> vsnrmadata
> 
> ExpressionSet (storageMode: lockedEnvironment)
> 
> assayData: 34760 features, 12 samples
> 
>   element names: exprs
> 
> protocolData
> 
>   sampleNames: 01_V12_1.CEL, 02_V12_2.CEL, ..., 12_D12_3.CEL  (12 total)
> 
>   varLabels and varMetadata description:
> 
>     ScanDate: NA
> 
> phenoData
> 
>   sampleNames: 01_V12_1.CEL, 02_V12_2.CEL, ..., 12_D12_3.CEL  (12 total)
> 
>   varLabels and varMetadata description:
> 
>     Treatment:
> 
> featureData: none
> 
> experimentData: use 'experimentData(object)'
> 
> Annotation: mogene10stv1
> 
> 
> 
>> fvsnrmadata = nsFilter(vsnrmadata, require.entrez = TRUE, require.GOBP = FALSE, require.GOCC = FALSE, require.GOMF = FALSE, var.filter = FALSE)$eset
> 
> Error: getAnnMap: package mogene10stv1 not available
> 
> 
> 
>> sessionInfo()
> 
> R version 2.11.0 (2010-04-22)
> 
> i386-pc-mingw32
> 
> 
> 
> locale:
> 
> [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C
> 
> [5] LC_TIME=English_United Kingdom.1252
> 
> 
> 
> attached base packages:
> 
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> 
> 
> other attached packages:
> 
>  [1] limma_3.4.0                 mogene10stprobeset.db_5.0.1 org.Mm.eg.db_2.4.1          RSQLite_0.8-4               DBI_0.2-5                   AnnotationDbi_1.10.0
> 
>  [7] genefilter_1.30.0           vsn_3.16.0                  mogene10stv1cdf_2.6.0       affy_1.26.0                 Biobase_2.8.0
> 
> 
> 
> loaded via a namespace (and not attached):
> 
> [1] affyio_1.16.0         annotate_1.26.0       grid_2.11.0           lattice_0.18-5        preprocessCore_1.10.0 splines_2.11.0        survival_2.35-8       tools_2.11.0
> 
> [9] xtable_1.5-6
> 
> 
> 
> 
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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