[BioC] tiling array normalization

[Lana Schaffer]

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 at 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.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
>