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

[James W. MacDonald]

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
>
>
> --
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>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
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Seattle WA 98105-6099