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

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