hey all, hi all, i am trying to normalize ,segment and process gene expression data using r version 2.15.1 iam stuck at nomalization where in i have tried the following commands. > library(snapCGH) >library(marray) >library(convert) >folder <- 'C:/man/' >file <- sort (dir(folder)) >o <- order(as.numeric(sub( 'OC ', '', sub('.txt', '', file)))) >file <- file[o] >data <- read.Agilent(fnames=file) >p <- order(data@maGnames@maInfo$ProbeName) >data <- data[p,] >normData <- maNorm(data) >normData@maLayout@maSub <- TRUE >normData@maLayout@maNspots <- nrow(normData@maM) >ma <- as(normData, 'MAList') >source('readPositionalInfo.R') > ma <- readPositionalInfo(ma, source='agilent') ## this command returned me this error Error in readPositionalInfo(ma, source = "agilent") : duplicate switch defaults: 'stop("Sour...' and '' what does this mean and how to proceed after this??? i also made a cloneinfo.txt file in the following format *Block Row Col Chr Position* and saved in excel as txt file (tab delimitted). it also gave me an error as > source('cloneinfo.txt') Error in source("cloneinfo.txt") : cloneinfo.txt:1:9: unexpected symbol 1: Block Row ^ how shall i rectify it? any help shall be greatly appreciated thanks Adesh [[alternative HTML version deleted]]

On Fri, Aug 24, 2012 at 9:17 AM, adesh ashok <adesh.ashok.7@gmail.com>wrote: > hey all, > hi all, > i am trying to normalize ,segment and process gene expression data using r > version 2.15.1 > iam stuck at nomalization where in i have tried the following commands. > > > library(snapCGH) > > >library(marray) > > >library(convert) > > >folder <- 'C:/man/' > > >file <- sort (dir(folder)) > > >o <- order(as.numeric(sub( 'OC ', '', sub('.txt', '', file)))) > > >file <- file[o] > > >data <- read.Agilent(fnames=file) > > >p <- order(data@maGnames@maInfo$ProbeName) > > >data <- data[p,] > > >normData <- maNorm(data) > > >normData@maLayout@maSub <- TRUE > > >normData@maLayout@maNspots <- nrow(normData@maM) > > >ma <- as(normData, 'MAList') > > >source('readPositionalInfo.R') > > > ma <- readPositionalInfo(ma, source='agilent') ## this command > returned me this error > Error in readPositionalInfo(ma, source = "agilent") : > duplicate switch defaults: 'stop("Sour...' and '' > > > what does this mean and how to proceed after this??? > > i also made a cloneinfo.txt file in the following format > > *Block Row Col Chr Position* > > and saved in excel as txt file (tab delimitted). it also gave me an error > as > > > source('cloneinfo.txt') > Hi, Adesh. Please read the help for source() (type ?source into R). You will need to use something like read.table() instead (type ?read.table into R for details). Sean > Error in source("cloneinfo.txt") : cloneinfo.txt:1:9: unexpected symbol > 1: Block Row > ^ > > how shall i rectify it? > > any help shall be greatly appreciated > > thanks > Adesh > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]