Hi Marcos, It seems from your code that you already know this, but I'll state it for the archives: you can put a variety of annotation information in fit$genes, and all of it will be automatically pulled into the output of topTable, which is handy if you'll be using topTable for several different contrasts. You already had this in your code to add the gene symbols: > fit2$genes$Symbol=getSYMBOL(fit2$genes$ID, "hgu133plus2") You can add as many other columns as you want: > fit2$genes$EG <- getEG(fit2$genes$ID, "hgu133plus2") > fit2$genes$GeneName <- unlist(mget(fit$genes$ID, hgu133plus2GENENAME)) etc. Cheers, Jenny At 03:56 PM 10/6/2009, James W. MacDonald wrote: >Please don't take things off-list. > >Marcos Pinho wrote: >>Jim, >> >>thanks for your reply. I was already able to >>introduce gene symbols. What I was looking for >>was to somehow create a column with short gene names for my final report. > >There isn't a getShortName() in annotate, but it >isn't difficult to get these data directly: > >names <- unlist(mget(fit$genes$ID, hgu133plus2GENENAME)) > >see ls("package:hgu133plus2.db") for all the annotation possibilities. > >Best, > >Jim > > >> >>cheers, >> >>Marcos >> >>*> library(limma)* >>*> fit =lmFit (esetF, design)* >>*> fit2=eBayes(fit)* >>*> library(annotate)* >>Loading required package: xtable >> >>Attaching package: 'xtable' >> >> >> The following object(s) are masked from package:widgetTools : >> >> label >> >>*> fit2$genes$Symbol=getSYMBOL(fit2$genes$ID, "hgu133plus2")* >>*> topTable(fit2, coef=2)* >>* * >>*fit2$genes$EG <- getEG(fit2$genes$ID, "hgu133plus2")*** >> ID Symbol logFC AveExpr t P.Value >>adj.P.Val >>5253 209993_at ABCB1 8.167898 6.410285 28.41936 1.387084e-06 0.008649451 >>3378 1553436_at MUC19 7.512443 6.097913 25.70956 2.249499e-06 0.008649451 >>9828 206488_s_at CD36 7.318355 6.081049 22.79634 4.015521e-06 0.008649451 >>6995 222392_x_at PERP 6.047929 6.736659 20.28712 7.035669e-06 0.008649451 >>8973 210603_at ARD1B 6.088776 5.773605 20.23547 7.122355e-06 0.008649451 >>1412 235683_at SESN3 6.589716 5.620394 20.17661 7.222719e-06 0.008649451 >>7573 216191_s_at TRD@ -6.153962 5.640399 -19.71517 8.071494e-06 0.008649451 >>4013 202948_at IL1R1 -6.231328 5.580407 -19.61010 8.281240e-06 0.008649451 >>5302 205934_at PLCL1 5.836512 5.809832 19.53496 8.435274e-06 0.008649451 >>4061 205786_s_at ITGAM -6.788839 7.957034 -18.03301 1.238036e-05 0.008649451 >>On Tue, Oct 6, 2009 at 4:18 PM, James W. >>MacDonald <jmacdon at="" med.umich.edu="" <mailto:jmacdon="" at="" med.umich.edu="">> wrote: >> Hi Marcos, >> >> Marcos Pinho wrote: >> Dear list, >> can anybody suggest how could I insert gene names in additional >> to gene >> symbols on my topTable generated by limma with my differentially >> expressed >> genes? >> >> It really depends on what annotation you have for your genes. >> However the general idea would be to use one of the org.Xx.eg.db >> packages to annotate your genes, or if you are using a commercial >> chip, use a chip-specific annotation package. >> Say your MArrayLM object is called 'fit' >> tabl <- topTable(fit) ##maybe need a coef argument as well. >> if you have Entrez Gene IDs >> tabl$Genes <- unlist(mget(tabl$ID, org.Xx.eg.dbSYMBOL)) >> if you have an affy chip >> tabl$Genes <- unlist(mget(tabl$ID, theaffychipSYMBOL)) >> or so. >> Does that help? >> Best, >> Jim >> >> cheers, >> Marcos B. Pinho >> Programa de Engenharia Qu?mica - PEQ >> Laborat?rio de Engenharia de Cultivos Celulares- LECC >> Universidade Federal do Rio de Janeiro - UFRJ >> Instituto Nacional de C?ncer - INCA >> Rio de Janeiro - Brasil >> [[alternative HTML version deleted]] >> >> >>-------------------------------------------------------------------- ---- >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> <mailto:bioconductor at="" stat.math.ethz.ch=""> >> 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 >> >> >>-- >>Marcos B. Pinho >>Programa de Engenharia Qu?mica - PEQ >>Laborat?rio de Engenharia de Cultivos Celulares- LECC >>Universidade Federal do Rio de Janeiro - UFRJ >>Instituto Nacional de C?ncer - INCA >>Rio de Janeiro - Brasil > >-- >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 > >_______________________________________________ >Bioconductor mailing list >Bioconductor at stat.math.ethz.ch >https://stat.ethz.ch/mailman/listinfo/bioconductor >Search the archives: >http://news.gmane.org/gmane.science.biology.informatics.conductor Jenny Drnevich, Ph.D. Functional Genomics Bioinformatics Specialist W.M. Keck Center for Comparative and Functional Genomics Roy J. Carver Biotechnology Center University of Illinois, Urbana-Champaign 330 ERML 1201 W. Gregory Dr. Urbana, IL 61801 USA ph: 217-244-7355 fax: 217-265-5066 e-mail: drnevich at illinois.edu