Dear List, could anybody help on how to insert columns in TopTable for entrez gene id, gene name and symbol when using the hugene1.0ST arrays. When using the regular 3'IVT arrays such as the hgu133plus2 I used the following lines without a problem > *ebayes$genes$Symbol=getSYMBOL(ebayes$genes$ID, "hgu133plus2")* > *ebayes$genes$EG <- getEG(ebayes$genes$ID, "hgu133plus2")* > *ebayes$genes$GeneName <- unlist(mget(fit$genes$ID, hgu133plus2GENENAME))* Unfortunately it is not working with my hugene1.0st files. Any suggestions? Regards, -- Marcos B. Pinho Programa de Engenharia Química - PEQ Laboratório de Engenharia de Cultivos Celulares- LECC Universidade Federal do Rio de Janeiro - UFRJ Instituto Nacional de Câncer - INCA Rio de Janeiro - Brasil [[alternative HTML version deleted]]

Hi Marcos, On 12/3/2010 8:32 AM, Marcos Pinho wrote: > Dear List, > > could anybody help on how to insert columns in TopTable for entrez gene id, > gene name and symbol when using the hugene1.0ST arrays. > > When using the regular 3'IVT arrays such as the hgu133plus2 I used the > following lines without a problem > >> *ebayes$genes$Symbol=getSYMBOL(ebayes$genes$ID, "hgu133plus2")* > > > >> *ebayes$genes$EG<- getEG(ebayes$genes$ID, "hgu133plus2")* > > > >> *ebayes$genes$GeneName<- unlist(mget(fit$genes$ID, hgu133plus2GENENAME))* > > > Unfortunately it is not working with my hugene1.0st files. > > Any suggestions? It depends on how you are analyzing your hugene chips, but you will want to use either the hugene10sttranscriptcluster.db or hugene10stprobeset.db packages. Best, Jim > > Regards, > > > > > _______________________________________________ > 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