Hello All

I am trying to work on ArrayCGH analysis.

My goal is to find regions of gains and loss in the array to find those
regions and plot them.

I am planning to use snapCGH and cghMCR library available in the
bioconductor website.
I realize that the examples are given for "Agilent array" and the other one
for "GeneChip" array.

So I was using some example from this link and ran into few errors

https://stat.ethz.ch/pipermail/bioconductor/2006-October/014724.html

apparently after I have read the data into an RGlist but I cannot get the
positional info by using the command

RG <- readPositionalInfo(RG, source = "nimblegen")
giving errors

> RG <- readPositionalInfo(RG, source = "nimblegen")
Warning message:
In data.frame(input$genes, Chr = as.numeric(chr), Start =
(as.numeric(start)/1e+06),  :
  NAs introduced by coercion



Following is the code I used


library(snapCGH)
library(limma)
library(IDPmisc)

source("NimblegenUtilityFunctions.R")

NimRootDir <- getwd()

samplekey <- readSampleKey(path = NimRootDir,  row.names = NULL)

data.files <-
  NimblegenTargetFiles(samplekey,
                       path = paste(NimRootDir,
                         "/Raw_Data_Files",
                         sep=""))

targets <- as.data.frame(NimblegenTargets(samplekey, path = NimRootDir))
RG <- read.nimblegen(files = data.files)
RG$design <- c(-1,-1)

This is how my RGList looks like

> RG
An object of class "RGList"
$R
     63133702_532 63132902_532
[1,]          721          699
[2,]          563          666
[3,]         1427         1391
[4,]         4040         3735
[5,]          522          540
719591 more rows ...

$G
     63133702_532 63132902_532
[1,]          897          831
[2,]          729          657
[3,]         1326         1105
[4,]         4195         2003
[5,]          575          673
719591 more rows ...

$Rb
     63133702_532 63132902_532
[1,]            0            0
[2,]            0            0
[3,]            0            0
[4,]            0            0
[5,]            0            0
719591 more rows ...

$Gb
     63133702_532 63132902_532
[1,]            0            0
[2,]            0            0
[3,]            0            0
[4,]            0            0
[5,]            0            0
719591 more rows ...

$genes
         IMAGE_ID GENE_EXPR_OPTION           SEQ_ID         PROBE_ID
POSITION   X    Y MATCH_INDEX SEQ_URL
1673 63133702_532           BLOCK1 chr10:1-20806668 CHR10FS000003241
3241 648 1180   244162334      NA
1674 63133702_532           BLOCK1 chr10:1-20806668 CHR10FS000005127
5127 524 1076   244162335      NA
1675 63133702_532           BLOCK1 chr10:1-20806668 CHR10FS000008662
8662 978 1246   244162336      NA
1676 63133702_532           BLOCK1 chr10:1-20806668 CHR10FS000012642
12642 265  265   244162337      NA
1677 63133702_532           BLOCK1 chr10:1-20806668 CHR10FS000019792
19792 878  496   244162338      NA
719591 more rows ...

$design
[1] -1 -1


Any help will be greatly appreciated.

Regards


M. Haque
Center for Reproductive Biology
School of Biological Sciences
Washington State University
Pullman, WA

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