Thank you, Bernd! and of course Jim!! :)



On Wed, May 7, 2014 at 6:22 PM, Bernd Klaus <bernd.klaus@embl.de> wrote:

> Hi Ninni,
>
> no, you need to switch, there is an annotation data base for every single
> platform (thanks to Jim MacDonald!), search here:
>
> http://bioconductor.org/packages/release/BiocViews.html#___AnnotationData
>
> The 1.0 one is here:
>
> http://bioconductor.org/packages/release/data/annotation/htmlhugene10sttranscriptcluster.db.html
>
> Best wishes,
>
> Bernd
>
> On Wed, 7 May 2014 18:17:19 +0200
> Ninni Nahm <ninninahm@gmail.com> wrote:
>
> > Thank you! That was very very helpful!
> > I wanted to ask if I can use the hugene20sttranscriptcluster.db package
> for
> > all hugene arrays? I have one more to analyze, which is a st 1 array.
> > Best
> > Ninni
> >
> >
> >
> > On Wed, May 7, 2014 at 2:57 PM, Bernd Klaus <bernd.klaus@embl.de> wrote:
> >
> > > Hi Ninni,
> > >
> > > I guess a very simple workflow would be:
> > >
> > > 1.read celfiles
> > > library(oligo)
> > > rawData = read.celfiles(< character vector of celfiles >)
> > >
> > > 2. perform RMA and get "transcript cluster" summarized data back
> > >  using only "core" genes ("safely" annotated genes according to affy)
> > >  this is the default in oligo.
> > >
> > > Eset = rma(rawData,target="core")
> > >
> > > 3. Load annotation package and annotate "transcript clusters" with some
> > > stuff contained in that package.
> > >
> > > ## load Annotation package
> > > library("hugene20sttranscriptcluster.db")
> > >
> > >         annotateGene = function ( db , what , missing ) {
> > >         tab = toTable(db[intersect(featureNames(Eset),
>  mappedkeys(db)) ])
> > >         mt = match ( featureNames ( Eset ) , tab$probe_id )
> > >         ifelse ( is.na(mt), missing , tab[[ what ]][ mt ])
> > >         }
> > >
> > >
> > > fData(Eset)$symbol = annotateGene( hugene20sttranscriptclusterSYMBOL
> > > ,"symbol" , missing = NA )
> > > fData(Eset)$genename = annotateGene(
> hugene20sttranscriptclusterGENENAME ,
> > > "gene_name" , missing = NA )
> > > fData(Eset)$ensembl = annotateGene( hugene20sttranscriptclusterENSEMBL
> ,
> > > "ensembl_id" , missing = NA )
> > >
> > >
> > > 4. After that keep only the "transcript clusters"  that have a ENSEMBL
> > > Gene ID.
> > > (for example)
> > >
> > >
> > > Hope that helps,
> > >
> > > Bernd
> > >
> > > On Wed,  7 May 2014 05:06:00 -0700 (PDT)
> > > "Ninni Nahm \[guest\]" <guest@bioconductor.org> wrote:
> > >
> > > >
> > > > Hi all!
> > > >
> > > > I am feeling a little bit stupid, but I have been searching for two
> days
> > > now (maybe I search wrong?!) and could not figure it out.
> > > > I want to analyze a Human Gene st array.
> > > > I know that there is the oligo package, I found this annotation
> package
> > > here pd.hugene.2.0.st, but, I do not know how to do the steps. I am
> used
> > > to the affy package and affy pipelines.
> > > > All I find when searching for solutions are ways on how to make your
> own
> > > annotation package, that is not necessary, I think, because I found the
> > > pd.hugene.2.0.st. Or am I wrong? Somehow I can t use it in the same
> way
> > > as I do with the for example hgu133a.db package that provides me the
> > > annotations.
> > > >
> > > > Im really lost...
> > > >
> > > > I want to do:
> > > >
> > > > - probe level analysis (similar to affyplm)
> > > > - RMA normalization (Somehow oligo does this, I think)
> > > > - Filter probes that are controls (as one does with affy: AFFX, for
> > > hgu133a)
> > > > - annotation of probesets (normally, I would use the IQR filter to
> get
> > > unique entrez ids, but how do I do this with the ST array?)
> > > >
> > > >
> > > > I know that there is something about probe and transcript to be
> aware of
> > > and core? But I cannot connect the workflow.
> > > >
> > > > I would be so happy if someone helped me, pointed me to the right
> docs.
> > > (the oligo userguide is not so helpful for me because I still dont
> > > understand what to do with what and when...) Sorry!
> > > >
> > > > Thanks!
> > > >
> > > > Ninni
> > > >
> > > >  -- output of sessionInfo():
> > > >
> > > > -
> > > >
> > > > --
> > > > Sent via the guest posting facility at bioconductor.org.
> > > >
> > > > _______________________________________________
> > > > Bioconductor mailing list
> > > > Bioconductor@r-project.org
> > > > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > > > Search the archives:
> > > http://news.gmane.org/gmane.science.biology.informatics.conductor
> > >
>

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