Wolfgang,
I have implemented your normalization code from your vignette with some of our data.  I would like to 
demonstrate your normalization results by looking at genes RPN2 and SER33.  After calling your
function comparisonPlot, I am not seeing the "ps" file.  Would you be able to help figure out why I can't
get the postscript file?  (I am not familiar with the function of "[" for lapply.)
R version 2.4.0 (2006-10-03) 
i686-redhat-linux-gnu 

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
 [1] "splines"   "grid"      "tools"     "methods"   "stats"     "graphics" 
 [7] "grDevices" "utils"     "datasets"  "base"     

other attached packages:
 davidTiling           GO  tilingArray       pixmap  geneplotter     annotate 
     "1.2.1"     "1.10.0"     "1.12.0"      "0.4-5"     "1.12.0"     "1.12.1" 
  genefilter     survival          vsn  strucchange     sandwich          zoo 
    "1.12.0"       "2.29"     "1.12.0"      "1.3-1"      "2.0-1"      "1.2-2" 
RColorBrewer         affy       affyio      Biobase 
     "0.2-3"     "1.12.2"      "1.2.0"     "1.12.2" 

VY=readCel2eSet(fns,path=celpath)
library(davidTiling)
data("probeAnno")
whPM = PMindex(probeAnno)
whBG = BGindex(probeAnno)
length(whPM)
length(whBG)
all(whBG %in% whPM)
VY$nucleicAcid <- c("DNA","total RNA","total RNA","total RNA","total RNA")
isDNA = VY$nucleicAcid %in% "DNA"
isRNA = VY$nucleicAcid %in% "total RNA"
pfn = sprintf("assessNorm-normalize%d.pdf", seq(along = which(isRNA)))
xn2 = normalizeByReference(VY[,isRNA], VY[,isDNA], 
  pm=whPM, background=whBG, plotFileNames=pfn)
#  found the plotFiles in the directory
xn1 = normalizeByReference(VY[,isRNA],VY[,isDNA],pm=whPM,background=whBG,cutoffQuantile=0)
sta = probeAnno$"9.-.start"
end = probeAnno$"9.-.end"
ind=probeAnno$"9.-.index"
dat = vector(mode = "list", length = 5)
dat[[1]] = log2(exprs(VY)[ind, which(isDNA)[1]])
dat[[2]] = log2(exprs(VY)[ind, which(isRNA)[1]])
dat[[3]] = dat[[2]] - dat[[1]]
dat[[4]] = exprs(xn1)[ind, 1]
dat[[5]] = exprs(xn2)[ind, 1]
dat[[6]] = exprs(xn2)[ind, 1]
for (j in 3:length(dat)) dat[[j]] = dat[[j]] - quantile(dat[[j]],0.05, na.rm = TRUE)
names(dat) = letters[seq(along=dat)]
sel = (sta >= 216600 & end <= 227000)
ysc = sapply(dat, function(py) quantile(py, probs = c(0,1),na.rm=TRUE))
ysc[,3:6] = c(-3,8)
anno = data.frame(start=c(217860, 221078),end =c(220297,222487),name=I(c("RPN2","SER33")))
ticks = c(217,223,224,225,226)
comparisonPlot((sta+end)[sel]/2,lapply(dat,"[",sel),yscale=ysc,anno=anno,ticks=ticks,cex=0.2)

Lana Schaffer
Biostatistics/Informatics
The Scripps Research Institute
DNA Array Core Facility
La Jolla, CA 92037
(858) 784-2263
(858) 784-2994
schaffer@scripps.edu



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