Hi, I’m not sure whether it’s directly related to Bioconductor. Even if it’s not, I would appreciate if I could get some pointers. When I normalize a set of cDNA dataset (patients), I come up with several repeated gene-Ids that have different expression values. Wonder how to deal with (combine!) these cDNA gene-repeats such that ultimately one gene refers only to one expression-value per patient. Thank you. Kind regards, Chintanu [[alternative HTML version deleted]]

hello chintanu, You are very much right. Your query isn't related to use of Bioconductor. I'm not sure whether you are talking about cDNA microarray data or just cDNA counts from a cDNA library. Nevertheless, those repeated gene-Ids (different expression values) are due to alternative transcripts. Due to different exon constitution and/ or different UTR lengths, alternative transcripts would have variable stability and also functional repertoire. So it is for you to take the call as to whether average out the alternative transcripts to make downstream analysis simpler or do a transcript- wise analysis and take account of the actual variability in the cell. regards, amit mandal Graduate student Genomics & Molecular Medicine Lab IGIB Delhi On Mon, Aug 31, 2009 at 11:23 AM, Chintanu <chintanu@gmail.com> wrote: > Hi, > > I’m not sure whether it’s directly related to Bioconductor. Even if it’s > not, I would appreciate if I could get some pointers. > > When I normalize a set of cDNA dataset (patients), I come up with several > repeated gene-Ids that have different expression values. Wonder how to deal > with (combine!) these cDNA gene-repeats such that ultimately one gene > refers > only to one expression-value per patient. > > Thank you. > > Kind regards, > > Chintanu > > [[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 > -- --------------------------------------------------------------- The robbed that smiles, steals something from the thief. - Shakespeare --------------------------------------------------------------- [[alternative HTML version deleted]]