This is one option: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/gen omic_curated_CDF.asp Paul. On Tue, Mar 15, 2011 at 4:43 PM, Wendy Qiao <wendy2.qiao at="" gmail.com=""> wrote: > Thank you, James. > > Sorry, I did not make my question clear. > > What I meant is that, on a chip, there are multiple probes for the same > gene. I was wondering if there is a package or command that can combine the > expression values on multiple probes for the same gene to one value by > taking the median or average. It is not hard to write the code for doing > this, but I was just wondering if there is existing package for doing this. > > Wendy > > On 15 March 2011 12:03, James W. MacDonald <jmacdon at="" med.umich.edu=""> wrote: > >> Hi Wendy, >> >> >> On 3/15/2011 11:30 AM, Wendy Qiao wrote: >> >>> Hi all, >>> >>> I am searching for a Bioconductor package that can collapse affymetrix >>> probe >>> id to gene symbols or entrez id, but I have not had any luck yet. Does >>> anyone know any package that can collapse the probe id to gene symbols? >>> >> >> What exactly do you mean by 'collapse the probe id to gene symbol'? There >> are annotation packages for pretty much all of the Affy chips that will map >> probesets to either Entrez Gene ID or gene symbol (e.g., for the >> HG-U133Plus2 chip we have the hgu133plus2.db package). These provide the >> mappings in a simple way, using either get() or mget(): >> >> > get("1007_s_at", hgu95av2ENTREZID) >> [1] "780" >> > get("1007_s_at", hgu95av2GENENAME) >> [1] "discoidin domain receptor tyrosine kinase 1" >> > get("1007_s_at", hgu95av2SYMBOL) >> [1] "DDR1" >> >> But maybe you are looking for something else? >> >> Best, >> >> Jim >> >> >> >>> Thank you in advance, >>> Wendy >>> >>> ? ? ? ?[[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should not be >> used for urgent or sensitive issues >> > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Paul Geeleher (PhD Student) School of Mathematics, Statistics and Applied Mathematics National University of Ireland Galway Ireland -- www.bioinformaticstutorials.com

Hi Wendy, for something like this the function aggregate should do the job. type ?aggregate in R for more details. Yong Li Wendy Qiao wrote: > Thank you, James. > > Sorry, I did not make my question clear. > > What I meant is that, on a chip, there are multiple probes for the same > gene. I was wondering if there is a package or command that can combine the > expression values on multiple probes for the same gene to one value by > taking the median or average. It is not hard to write the code for doing > this, but I was just wondering if there is existing package for doing this. > > Wendy > > On 15 March 2011 12:03, James W. MacDonald <jmacdon at="" med.umich.edu=""> wrote: > >> Hi Wendy, >> >> >> On 3/15/2011 11:30 AM, Wendy Qiao wrote: >> >>> Hi all, >>> >>> I am searching for a Bioconductor package that can collapse affymetrix >>> probe >>> id to gene symbols or entrez id, but I have not had any luck yet. Does >>> anyone know any package that can collapse the probe id to gene symbols? >>> >> What exactly do you mean by 'collapse the probe id to gene symbol'? There >> are annotation packages for pretty much all of the Affy chips that will map >> probesets to either Entrez Gene ID or gene symbol (e.g., for the >> HG-U133Plus2 chip we have the hgu133plus2.db package). These provide the >> mappings in a simple way, using either get() or mget(): >> >>> get("1007_s_at", hgu95av2ENTREZID) >> [1] "780" >>> get("1007_s_at", hgu95av2GENENAME) >> [1] "discoidin domain receptor tyrosine kinase 1" >>> get("1007_s_at", hgu95av2SYMBOL) >> [1] "DDR1" >> >> But maybe you are looking for something else? >> >> Best, >> >> Jim >> >> >> >>> Thank you in advance, >>> Wendy >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> Douglas Lab >> University of Michigan >> Department of Human Genetics >> 5912 Buhl >> 1241 E. Catherine St. >> Ann Arbor MI 48109-5618 >> 734-615-7826 >> ********************************************************** >> Electronic Mail is not secure, may not be read every day, and should not be >> used for urgent or sensitive issues >> > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >