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. This e-mail message is confidential and for use by the addre...{{dropped}}

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. This e-mail message is confidential and for use by the addre...{{dropped}}