Thanks a lot. It is very helpful and I will look into the help pages as well. I am wondering how many "gene-based summary" in articles I read are actually "transcript-based summary". Most of these papers report differentially expressed "genes". When I met the first authors and asked them the question I posted here, they told me they did not do the analysis themselves and they don't have the answer for me. Finally, if I am going to do a transcript-based summary, basically I just need to use the differentially-regulated probeset numbers as the differentially-regulated transcript numbers, it this correct? Richie On Tue, Nov 17, 2009 at 10:05 AM, Marc Carlson <mcarlson@fhcrc.org> wrote: > Hi Cheng-Yuan, > > That expression just removes any unmapped entrez IDs (which will be > given as an NA), and then also removes any that are duplicated from the > list. However, this will only work for that case where your probeset > IDs are each mapped to one entrez gene ID each (a many to one > relationship between probes and genes). And by default, the annotation > packages will only display data for probesets that map like this. And > for most probes on most platforms, this will be perfectly adequate. > But, if you really want to explore the many to many mappings between > some genes and their more ambiguously designed probesets, then you need > to look at the help page for the toggleProbes() method in > AnnotationDbi. Using this method can allow you to expose these > relationships so that you can see the more troublesome probes. Once you > have done that, you will be able to see that some probes map to several > different genes (a many to many relationship). > > library(AnnotationDbi) > ?toggleProbes > > Should help a bit if you really want to go there. Let me know if you > have further questions, > > > Marc > > > > Cheng-Yuan Kao wrote: > > Hi, > > > > We have C. elegans expression data set. > > Do you know what exactly [!is.na(entrezIDs) & !duplicated(entrezIDs)] > does? > > > > Thanks. > > > > Cheng-Yuan > > > > On Tue, Nov 17, 2009 at 3:34 AM, Yuan Hao <yuan.hao@ucd.ie> wrote: > > > > > >> Hi Richie, > >> > >> I am not sure which data set and annotation package you are working on, > >> taking hgu133plus2 chip for example. if you just want to get Entrez > genes > >> corresponding to your probesets, you can simply do: > >> > >> library("hgu133plus2.db") > >> entrezIDs<-unlist(mget(probesets, hgu133plus2ENTREZID)) > >> entrezIDs<-entrezIDs[!is.na(entrezIDs) & !duplicated(entrezIDs)] > >> > >> Hope it is what you want. > >> > >> Cheers, > >> Yuan > >> > >> > >> > >> > >> On 17 Nov 2009, at 08:15, Tobias Straub wrote: > >> > >> hi richie, > >> > >>> one easy way to handle the multiple probesets per gene problem is to > keep > >>> only the one probeset with the highest variance across replicates. the > >>> 'nsFilter' function in the 'genefilter' package provides this operation > for > >>> ExpressionSet objects. > >>> using this filter approach you might of course miss some differentially > >>> regulated splicing events. > >>> > >>> best regards > >>> tobias > >>> > >>> > >>> On Nov 17, 2009, at 12:01 AM, Cheng-Yuan Kao wrote: > >>> > >>> Hi, there, > >>> > >>>> I have a question regarding Affy chip data. > >>>> > >>>> We did many expression arrays and used LIMMA to get the differentially > >>>> expressed "genes" (control vs treatment). > >>>> > >>>> However I found that some probesets have multiple genes according to > Affy > >>>> annotation file. > >>>> > >>>> On the other hand, multiple probesets could match to the same gene. > >>>> Even more, some probesets matched to the same gene could be regulated > in > >>>> different way. > >>>> > >>>> So actually what LIMMA gave us is differentially expressed > "probesets". > >>>> > >>>> Say we have 500 probesets up-regulated but we indeed want to know how > >>>> many > >>>> "genes" are up-regulated. > >>>> > >>>> I don't know how to reasonably convert the probesets to genes due to > the > >>>> non-one-to-one relationship. > >>>> > >>>> What's the convention in the microarray field? > >>>> > >>>> Any suggestion would be greatly appreciated. > >>>> > >>>> > >>>> Richie > >>>> > >>>> [[alternative HTML version deleted]] > >>>> > >>>> _______________________________________________ > >>>> Bioconductor mailing list > >>>> Bioconductor@stat.math.ethz.ch > >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>>> Search the archives: > >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor > >>>> > >>>> > >>> ---------------------------------------------------------------------- > >>> Dr. Tobias Straub ++4989218075439 Adolf-Butenandt-Institute, München D > >>> > >>> _______________________________________________ > >>> Bioconductor mailing list > >>> Bioconductor@stat.math.ethz.ch > >>> https://stat.ethz.ch/mailman/listinfo/bioconductor > >>> Search the archives: > >>> http://news.gmane.org/gmane.science.biology.informatics.conductor > >>> > >>> > >> > > > > [[alternative HTML version deleted]] > > > > > > ------------------------------------------------------------------ ------ > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > [[alternative HTML version deleted]]