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Wolfgang, I now have the X11() graphics command working. After the comparisonPlot function I am now getting: Error in grid.Call.graphics("L_text", x$label, x$x, x$y, resolveHJust(x$just, : X11 font at size 16 could not be loaded This must be some technical X11 problem. Lana ----- Original Message ----- From: "Wolfgang Huber" <huber@ebi.ac.uk> To: "Lana Schaffer" <schaffer at="" scripps.edu=""> Cc: <bioconductor at="" stat.math.ethz.ch=""> Sent: Thursday, January 25, 2007 2:42 PM Subject: Re: tiling array normalization > Dear Lana, > >> 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. > > Where did you get the idea that you should see a "ps" file? Neither the > man page of the function nor any other place I am aware of suggest that it > should produce one. It will create a plot on the current graphics device, > using grid graphics. Note that for any R graphics going e.g. to a > postscript device, you will need to call "dev.off()" before using the > postscript file. > > > Would you be able to help figure out why I can't >> get the postscript file? > > Please send a code example that I (and others) can run. Otherwise I will > not be able to help. The first line in your code example produces: > > > VY=readCel2eSet(fns,path=celpath) > Error in unique(c("AsIs", oldClass(x))) : object "fns" not found > >> (I am not familiar with the function of "[" for lapply.) > > lapply(dat,"[",sel) takes list dat and produces a new list where each > element has been subset using indices "sel". This functionality of R is > quite unrelated to writing postscript files. > > Best wishes > Wolfgang > >> 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.UT F-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 at scripps.edu >> >> >> > > > -- > ------------------------------------------------------------------ > Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber >

Wolfgang, Our DNA sample gives a signal centers around 6 and yours centers around 10. We only have one DNA sample right now. I am wondering how the DNA absolute signal values affect the calculation. Our RNA samples do not show unnormalized expression of RPN2 or SER33, but I will look at other genes. Thanks, Lana ----- Original Message ----- From: "Wolfgang Huber" <huber@ebi.ac.uk> To: "Lana Schaffer" <schaffer at="" scripps.edu=""> Cc: <bioconductor at="" stat.math.ethz.ch=""> Sent: Thursday, January 25, 2007 3:33 PM Subject: Re: tiling array normalization > Hi Lana, > > try > > options(warn=0) > > this should solve the problem, or you could install additional X-Windows > fonts on your machine. > > Best wishes > Wolfgang > > Schaffer wrote: >> Wolfgang, >> I now have the X11() graphics command working. >> After the comparisonPlot function I am now getting: >> Error in grid.Call.graphics("L_text", x$label, x$x, x$y, >> resolveHJust(x$just, : >> X11 font at size 16 could not be loaded >> This must be some technical X11 problem. >> Lana >> > -- > ------------------------------------------------------------------ > Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber >

Dear Lana, > 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. Where did you get the idea that you should see a "ps" file? Neither the man page of the function nor any other place I am aware of suggest that it should produce one. It will create a plot on the current graphics device, using grid graphics. Note that for any R graphics going e.g. to a postscript device, you will need to call "dev.off()" before using the postscript file. > Would you be able to help figure out why I can't > get the postscript file? Please send a code example that I (and others) can run. Otherwise I will not be able to help. The first line in your code example produces: > VY=readCel2eSet(fns,path=celpath) Error in unique(c("AsIs", oldClass(x))) : object "fns" not found > (I am not familiar with the function of "[" for lapply.) lapply(dat,"[",sel) takes list dat and produces a new list where each element has been subset using indices "sel". This functionality of R is quite unrelated to writing postscript files. Best wishes Wolfgang > 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_U S.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 at scripps.edu > > > -- ------------------------------------------------------------------ Wolfgang Huber EBI/EMBL Cambridge UK http://www.ebi.ac.uk/huber