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

James W. MacDonald jmacdon at uw.edu
Tue Apr 2 15:06:22 CEST 2013


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.
>
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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



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