Hello. Yes, it works!!!! Thanks, now I am working on how to design my analysis. Marcelo Em 15 de agosto de 2010 19:08, Benilton Carvalho <beniltoncarvalho at="" gmail.com=""> escreveu: > update > > vmd <- data.frame(labelDescription = "Treatment applied to samples") > > to > > vmd <- data.frame(labelDescription = "Treatment applied to samples", > channel=factor("_ALL_", levels=c("exprs", "_ALL_")) > > and let me know how it goes, > b > > 2010/8/15 Marcelo Brand?o <brandao.marcelo at="" gmail.com="">: >> Hi there >> Thanks for the script. >> But i think there is something broken or, probably, I am doing something wrong. >> Here is what I use: >> >>>source('http://bioconductor.org/biocLite.R') >> . >> . >> . >>>library(oligo) >> . >> . >> . >> =================================================================== ============= >> Welcome to oligo version 1.12.2 >> =================================================================== ============= >>> xys <- list.xysfiles() >>> ddf <- data.frame(group = rep(c("experimental", "control", "mutated"),each=4), row.names=xys) >>> vmd <- data.frame(labelDescription = "Treatment applied to samples") >>> pdt <- new("AnnotatedDataFrame", data=ddf, varMetadata=vmd) >>> rawData <- read.xysfiles(xys, phenoData=pdt) >> Loading required package: pd.2006.08.18.ti4932.60mer >> Loading required package: RSQLite >> Loading required package: DBI >> Platform design info loaded. >> Checking designs for each XYS file... Done. >> Allocating memory... Done. >> Reading 50186202_532.xys. >> Reading 50194302_532.xys. >> Reading 50194402_532.xys. >> Reading 50196202_532.xys. >> Reading 50198502_532.xys. >> Reading 50201302_532.xys. >> Reading 50204102_532.xys. >> Reading 50204202_532.xys. >> Reading 50204302_532.xys. >> Reading 50207902_532.xys. >> Reading 50208002_532.xys. >> Reading 50208102_532.xys. >> Error in validObject(out) : >> ?invalid class "ExpressionFeatureSet" object: >> ?'NChannelSet' varMetadata must have a 'channel' column >>> rawData$group >> Error: object 'rawData' not found >> >> It seems that I need a channel column somewhere. And here is my question, Where? >> >> Well, thanks for any help >> >> My best wishes >> >> Marcelo >> >> >> Em 13 de agosto de 2010 13:44, Benilton Carvalho >> <beniltoncarvalho at="" gmail.com=""> escreveu: >>> you should create the appropriate phenoData object and pass it to >>> read.xysfiles (if you're using 'oligo'). >>> >>> eg.: >>> >>> library(oligo) >>> xys <- list.xysfiles() >>> ddf <- data.frame(group = rep(c("experimental", "control", "mutated"), >>> each=4), row.names=xys) >>> vmd <- data.frame(labelDescription = "Treatment applied to samples") >>> pdt <- new("AnnotatedDataFrame", data=ddf, varMetadata=vmd) >>> rawData <- read.xysfiles(xys, phenoData=pdt) >>> rawData$group >>> >>> b >>> >>> 2010/8/13 Marcelo Brand?o <brandao.marcelo at="" gmail.com="">: >>>> Hello there >>>> I am using Bioc to analyze a Nimblegen Microarray. Everything seems to >>>> be smoothly working. I would like to ask for some help, I have 12 xys >>>> files, and wander if there is a way to "annotate" each one of them as >>>> experimental, control or mutated. So, when I will perform any >>>> comparison there is any way to design the experiment as designEsp <- >>>> cbind(Grp1=1,Grp2vs1=c(control,mutated)) ? >>>> >>>> Complicated? Well, to simplify: >>>> there is a way to simply say to Bioc: "now I will analyze control >>>> versus experimental." >>>> >>>> Many thanks in advance. >>>> >>>> Marcelo >>>> >>>> -- >>>> Marcelo Mendes Brand?o >>>> Postdoc fellow >>>> Laborat?rio de Biologia Molecular de Plantas - ESALQ/USP >>>> Website: http://bioinfo.esalq.usp.br >>>> AtPIN: http://bioinfo.esalq.usp.br/atpin >>>> SKYPE: mmbrand >>>> Tel: (+55) 19 3429 4442 >>>> >>>> _______________________________________________ >>>> 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 >>>> >>> >> >> >> >> -- >> Marcelo Mendes Brand?o >> Postdoc fellow >> Laborat?rio de Biologia Molecular de Plantas - ESALQ/USP >> Website: http://bioinfo.esalq.usp.br >> AtPIN: http://bioinfo.esalq.usp.br/atpin >> SKYPE: mmbrand >> Tel: (+55) 19 3429 4442 >> > -- Marcelo Mendes Brand?o Postdoc fellow Laborat?rio de Biologia Molecular de Plantas - ESALQ/USP Website: http://bioinfo.esalq.usp.br AtPIN: http://bioinfo.esalq.usp.br/atpin SKYPE: mmbrand Tel: (+55) 19 3429 4442