[BioC] SnapCGH problem

[Daniel Brewer]

I having trouble setting up Agilent 4100a array data to be used with
snapCGH.  This is what I do:

#Input file
targets <- readTargets()
stuff <- read.maimages(targets$FileName,source="agilent")

#Setup layout
stuff$genes$Block <- 1
names(stuff$genes)[2] <- "Column"
stuff$printer <- getLayout(stuff$genes)

#setup clone information
locData <- read.table(file="4100aLocationShort.csv", header=TRUE, sep="\t")
names(locData) <- c("ProbeName","Chromosome","Start","End")
stuff$genes <- merge(stuff$genes,locData, all.x=TRUE)
stuff$genes$Position <- stuff$genes$Start
stuff$genes$Chr <- stuff$genes$Chromosome

#Setup design (from snapCGH guide)
stuff$design <- c(-1,-1)

#Normalisation within
normed <- normalizeWithinArrays(stuff, method="loess")

#Get rid of "genes" with no location information
normed$genes <- normed$genes[!(is.na(normed$genes$Chr)) &
normed$genes$Chr != "",]

#ProcessCGH
normed2 <- processCGH(normed, method.of.averaging = mean,ID="ProbeName")

The result is:
> Averaging duplicated clones
> Processing chromosome  NA 
..
> Processing chromosome  NA 
> Warning messages:
> 1: > not meaningful for factors in: Ops.factor(MA$genes$Chr, maxChromThreshold) 
> 2: < not meaningful for factors in: Ops.factor(MA$genes$Chr, minChromThreshold) 
> 3: <= not meaningful for factors in: Ops.factor(uniq.chrom, maxChrom)

I was wondering whether you could help me solve this.  I can think of
two reasons why this might be occurring,
1) I have not deleted the data corresponding to the genes I have
removed.  Not sure how to do that.
2) My genes table is not set up correctly.  Here is a sample of the table:
    ProbeName Row Column ProbeUID ControlType
873   1000182  57     33     5912           0
874     10003   1     54       27           0
                                                                   GeneName
873                    actin related protein 2/3 complex, subunit 3 (21 kD)
874 Human (clone pAT 464) potential lymphokine/cytokine mRNA, complete cds.
    SystematicName Description Block Chromosome     Start       End
Position
873       BG483858      pSPORT     1         12 109335427 109350878
109335427
874         M25315       pBlue     1         17  31439709  31441605
31439709
    Chr
873  12
874  17


I appreciate your help

Daniel

-- 
**************************************************************

Daniel Brewer, Ph.D.

Institute of Cancer Research

Email: daniel.brewer at icr.ac.uk

**************************************************************

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP.

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