Hi averybody, how can I get easily from an MarrayLM object the ranking position in the toptable of a gene? Suppose I only know the ID... Apologies for the basic question. Regards. Emanuele [[alternative HTML version deleted]]

Hi, Is there a citation for GOstats other than > citation(package="GOstats") To cite package GOstats in publications use: R. Gentleman (2005). GOstats: Tools for manipulating GO and microarrays. R package version 1.1.3. Also, the only publication I could find using GOstats & Rgraphviz is Carey VJ, Gentry J, Whalen E, Gentleman R. Network structures and algorithms in Bioconductor. Bioinformatics. 2005 Jan 1;21(1):135-6. Epub 2004 Aug 5. are there any others? Thanks, Jeff __________________________________ Jeffrey Rasmussen Research Consultant, Bioinformatics Department of Immunology University of Washington

Dear Emanuele, Will this work? (I take from the toptable help, modify the last call to toptable, to add a genelist, assign it it an object, and then use which; substitute the "100" in toptable by the number of genes you do have). M <- matrix(rnorm(100*6,sd=0.3),100,6) M[1,1:3] <- M[1,1:3] + 2 design <- cbind(First3Arrays=c(1,1,1,0,0,0),Last3Arrays=c(0,0,0,1,1,1)) fit <- lmFit(M, design=design) fit <- eBayes(fit) mytable <- topTable(fit, genelist = paste("gene", 1:100, sep = "."), number = 100) which(mytable$ProbeID == "gene.8") Best, R. On Friday 20 May 2005 19:36, E.Marchi wrote: > Hi averybody, > how can I get easily from an MarrayLM object the ranking position in the > toptable of a gene? Suppose I only know the ID... Apologies for the basic > question. > Regards. > > Emanuele > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- Ram?n D?az-Uriarte Bioinformatics Unit Centro Nacional de Investigaciones Oncol?gicas (CNIO) (Spanish National Cancer Center) Melchor Fern?ndez Almagro, 3 28029 Madrid (Spain) Fax: +-34-91-224-6972 Phone: +-34-91-224-6900 http://ligarto.org/rdiaz PGP KeyID: 0xE89B3462 (http://ligarto.org/rdiaz/0xE89B3462.asc) **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en s...{{dropped}}