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
>
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>
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