Hello everyone,

I am trying to use the MANOR spatial normalisation package but I have got a problem

I get this 
message when i calculate the log2 ratios

Warning message:
NaNs produced in: log(x, base)

and when I try to normalise I get

Warning message:
NaNs produced in: log(x, base)

any help would be most appreciated

James

the script I am using:

require(MANOR)

## import GPR file
spot.names <- c("Name","ID","F635.Mean","F532.Mean","B635.Mean","B532.Mean")
ac <- import("C:/Documents and Settings/James_Morris/Desktop/R/test.csv.gpr",spot.names=spot.names, type="gpr", sep="\t")

## clone.names <- c("Clone","Chromosome","Position","Validation")
## read clone positions
pos <- read.table("C:/tmp/all_clones_mod_xy0.csv", sep=";", as.is=TRUE)
names(pos) <- c("Name", "Position", "Chromosome")

## merge both
ac$cloneValues<-pos
ac$id.rep<-"Name"

## compute a log-ratio
ac$arrayValues$Ratio<-(ac$arrayValues$F635.Mean-ac$arrayValues$B635.Mean)/(ac$arrayValues$F532.Mean-ac$arrayValues$B532.Mean)
ac$arrayValues$Ratio[ac$arrayValues$Ratio==Inf] <- NA
ac$arrayValues$LogRatio <- log(ac$arrayValues$Ratio,2)
## normalisation
data(flags)
local.spatial.flag$args <- alist(var = "LogRatio", by.var = NULL,nk = 5, prop = 0.25, thr = 1.2, beta = 1, family = "gaussian")
rep.flag$args$rep.thr <- 0.1

SNR.flag$snr.thr <-3
## add correct variable names for SNR.flag (signal to noise ratio)
SNR.flag$args$var.FG <- "F532.Mean"
SNR.flag$args$var.BG <- "B532.Mean"

amplicon.flag$ampli.ther <- 2

##flag.list <- list(spatial = local.spatial.flag, spot=spot.flag, SNR = SNR.flag, unique = unique.flag, amplicon = amplicon.flag, rep = rep.flag )
## same analysis without "unique.flag" and "replicate.flag"
## = what you did in CAPweb by using option "Exclude unique spots = No"
flag.list <- list(spatial = local.spatial.flag, spot=spot.flag, SNR = SNR.flag, amplicon = amplicon.flag, unique = unique.flag)

ac.norm <- norm.arrayCGH(ac, flag.list = flag.list, FUN = median, na.rm = TRUE)
ac.norm <- sort.arrayCGH(ac.norm)

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