Dear All, I make an exprSet using the read.exprSet function (see below). My file have 3575 genes, but I have 7 colunms (3 untreated replicates and 3 treated replicates). The first is the Gene_ID colunm. My procedure is correct? My doubt happened when I executed an eSet and I observed that it returned 7 samples. Does it consider the column gene_id as being a sample? > KarinaSusc<-read.table("Suscetivel_R.txt",header=TRUE,sep="\t",as.is =TRUE) > write.table(KarinaSusc, testFile, quote = FALSE, sep = "\t", row.names =TRUE, col.names = TRUE) > eSet <- read.exprSet(testFile) > eSet Expression Set (exprSet) with 3575 genes 7 samples phenoData object with 1 variables and 7 cases varLabels sample: arbitrary numbering Thanks a lot Marcelo > -----Original Message----- > From: Rafael A. Irizarry [mailto:ririzarr@jhsph.edu] > Sent: quinta-feira, 30 de outubro de 2003 00:52 > To: Marcelo Luiz de Laia > Cc: Ethz. Ch > Subject: Re: [BioC] Creating an new exprSet > > > the latest version of Biobase has a read.exprSet function you can use to > read in data. > > > > On Wed, 29 Oct 2003, Marcelo Luiz de Laia wrote: > > > Hi people, > > > > I read the Vignette of VSN and the html help for VSN and exprSet. > > > > I don't understand how do I do to create one new exprSet from my datas. > > > > Could Someone send me an exprSet model? > > How many files should I have? > > I have a 3 file (var_suscep_rep1.txt, var_suscep_rep2.txt, > > var_suscep_rep3.txt) with the following format: > > > > Gene_ID Ctrl_Bkgd Ctrl_sVol Ctrl_Vol Data_Bkgd Data_sVol Data_Vol > > gene1 30.2 1.9 32.2 7.4 1.1 8.4 > > > > Ctrl = Untreated > > Data = Treated > > Bkgd = background > > Vol = Intensity of foreground (spot) > > sVol = Vol - Bkgd > > > > Can I make a file with Ctrl_sVol and Data_sVol for each replicate or one > > file for Crtl_sVol and another file for Data_sVol? > > > > new('exprSet', > > exprs = ...., # What should I put here considering the data above? > > se.exprs = ...., # What should I put here considering the data above? > > phenoData = ...., # This a file? What should I put here > considering the data > > above? > > annotation = ...., # What should I put here considering the data above? > > description = ...., # What should I put here considering the data above? > > notes = ...., # What should I put here considering the data above? > > ) > > > > How do I do to load my datas into exprSet? > > > > Thanks > > > > Marcelo Luiz de Laia, M.Sc. > > Dep. de Tecnologia, Lab. Bioqu?mica e de Biologia Molecular > > Universidade Estadual Paulista - UNESP > > Via de Acesso Prof. Paulo Donato Castelane, Km 05 > > 14.884-900 - Jaboticabal, SP, Brazil > > PhoneFax: 16 3209-2675/2676/2677 R. 202/208/203 (trab.) > > Phone res: 16 3203 2328 - www.lbm.fcav.unesp.br - mlaia@yahoo.com > > --- > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > > > --- > Incoming mail is certified Virus Free. > Checked by AVG anti-virus system (http://www.grisoft.com). > Version: 6.0.532 / Virus Database: 326 - Release Date: 27/10/2003 > ---