[BioC] SnapCGH problem

[Daniel Brewer]

Just to answer my own question, the major problem was that my "Chr" was
a factors object rather than a numeric vector, so I used the less than
clear as.numeric(as.character(object)) to fix it.  It was also necessary
to convert the "X" and "Y"s to 23 and 24 respectively.

Daniel

Daniel Brewer wrote:
> 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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