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#___Annotatio nData > > The 1.0 one is here: > > http://bioconductor.org/packages/release/data/annotation/htmlhugene1 0sttranscriptcluster.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 > > > > [[alternative HTML version deleted]]