[BioC] faillure in ragene10stv1 in rat Gene St0.1 Affymetrix data

[James W. MacDonald]

Hi Antje,

Please don't take conversations off-list.

On 4/2/2013 9:27 AM, Antje Kammermeier wrote:
> Dear James,
>
> thank you for your answer.
>
> I successfully installed 'ragene10sttranscriptcluster.db'. 
> Unfortunately the error term  "getAnnMap: package ragene10stv1 not 
> available" stayed after  the R commans
> celfiles.filt<- nsFilter(Celfiles.norm,require.entrez=TRUE, var.cutoff 
> =0.5)$eset

If you re-read what I sent below, you will notice that you need to do 
two things, one of which you have neglected to do.

Best,

Jim


>
>
> 2013/4/2 James W. MacDonald <jmacdon at uw.edu <mailto:jmacdon at uw.edu>>
>
>     Hi Antje,
>
>
>     On 4/2/2013 4:07 AM, Antje Kammermeier [guest] wrote:
>
>         Dear team,
>
>         my name is Antje and I am nwe to Bioconductor. Hope all the
>         description is ok for you.
>         I analyse Rat Affymetrix data from Rat Gene ST 0.1 Data. I did
>         a normalisation and wanted to filter the data. I did all the
>         Installation for the Annotation data. Unfortunately I got the
>         error term ragene10stv1 not available. Can anybody what can be
>         wrong?
>
>
>         Thanks in foward
>
>
>         Antje
>
>           -- output of sessionInfo():
>
>         R command
>         celfiles<-ReadAffy()
>         Celfiles.norm<-rma(celfiles)
>
>
>     These arrays can be summarized at two different levels; at the
>     probeset (roughly exon) and transcript level. Well, not with the
>     affy package, but with ST-aware packages like oligo, xps, etc.
>     Because of this, there are two annotation packages for each array,
>     and you have to specify which one you are using.
>
>     Since you are using affy here, the summarization is at the
>     transcript level, so you want to do
>
>     annotation(Celfiles.norm) <- "ragene10sttranscriptcluster.db"
>
>     and ensure that you have this package installed, and everything
>     should proceed normally from here on out.
>
>     Best,
>
>     Jim
>
>
>         celfiles.filt<- nsFilter(Celfiles.norm,require.entrez=TRUE,
>         var.cutoff =0.5)$eset
>
>         Annotation packages installed
>         AnnotationDbi
>         pd.ragene.1.0.st.v1
>         ragene10stv1cdf
>         ragene10stv1probe
>
>
>         --
>         Sent via the guest posting facility at bioconductor.org
>         <http://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
>
>

-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099