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Version 1.8.1  (2003-11-21), ISBN 3-900051-00-3

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> invisible(options(echo = TRUE))
> library(affycomp)
Welcome to Bioconductor 
	 Vignettes contain introductory material.  To view, 
	 simply type: openVignette() 
	 For details on reading vignettes, see
	 the openVignette help page.
> library(tools)
> library(modreg)
> dilution.ngenes <- 0
> spikein.ngenes <- 0
> spikein133.ngenes <- 0
> ###read in nickname and other info
> affycomp.info <- read.table("info.txt",sep="\t",as.is=TRUE,quote="")
> method.name <- affycomp.info[3,2]
> verbose <- TRUE
> 
> # Read in the 3 files and perform assessments (if files exist).
> 
> f <- "dilution.csv"
> if(file.exists(f)){
+   d <- read.dilution(f)
+   if(verbose) cat("Performing 3 assessments on dilution data...")
+   dilution.assessment <- assessDilution(d,method.name=method.name)
+  # added by HJ - Jan 13, 04
+  tmp.assessment <- c(Dilution=list(dilution.assessment))
+   if(verbose) cat("\n")
+   dilution.ngenes <- nrow(exprs(d))
+ }
Performing 3 assessments on dilution data...
>    
> f <- "hgu95.csv"
> if(file.exists(f)){
+   s <- read.spikein(f,"hgu95a")
+   spikein.assessment <-
+     assessSpikeIn(s,verbose=verbose,method.name=method.name)
+   if(exists("dilution.assessment")){
+     tmp.assessment <- c(Dilution=list(dilution.assessment),spikein.assessment)
+     tmp.assessment["what"] <- "All"
+   }
+   spikein.assessment2 <-
+     assessSpikeIn2(s,verbose=verbose,method.name=method.name)
+   spikein.ngenes <- nrow(exprs(s))
+ }
> 
> f <- "hgu133.csv"
> if(file.exists(f)){
+   s <- read.spikein(f,"hgu133a")
+   spikein.assessment.133 <-
+     assessSpikeIn(s,verbose=verbose,method.name=method.name)
+   spikein.assessment2.133 <-
+     assessSpikeIn2(s,verbose=verbose,method.name=method.name)
+   spikein133.ngenes <- nrow(exprs(s))
+ }
Performing 6 assessments that will take a few minutes......
Performing 3 assessments that will take a few seconds...
> 
> # Now, if correct assessment lists exist we run Sweave and make tables.
> dir <- paste(.path.package("affycomp"),"Rnw",sep="/")
> 
> F1 <- exists("dilution.assessment")
> F2 <- exists("spikein.assessment")
> F3 <- exists("spikein.assessment.133")
> 
> Table <- matrix(NA,23,1)
> 
> if(F1 & F2){
+   Table <- tableAll(tmp.assessment)
+   
+   Table2 <- rbind(tableAll(spikein.assessment),
+                   tableAll(spikein.assessment2))
+   
+   results2 <- "results2.txt"
+   Table2 <- rbind(Table2,spikein.ngenes)
+   write(Table2,file=results2,ncol=1)
+   
+   Sweave(paste(dir,"comparison.Rnw",sep="/"))
+   Sweave(paste(dir,"simple.Rnw",sep="/"))
+   Sweave(paste(dir,"complete-assessment.Rnw",sep="/"))
+ }
> 
> if(F1 & !F2){
+   Table[1:6,] <- tableAll(dilution.assessment)
+   
+   Sweave(paste(dir,"dilution-assessment.Rnw",sep="/"))
+ }
Writing to file dilution-assessment.tex
Processing code chunks ...
 1 : term hide
 2 : term verbatim
 3 : term verbatim
 4 : term verbatim eps pdf
 5 : term verbatim eps pdf
 6 : term verbatim eps pdf

You can now run LaTeX on dilution-assessment.tex 
> 
> if(!F1 & F2){
+   Table[7:23,] <- tableAll(spikein.assessment)
+   Table2 <- rbind(tableAll(spikein.assessment),
+                   tableAll(spikein.assessment2))
+ 
+   results2 <- "results2.txt"
+   Table2 <- rbind(Table2,spikein.ngenes)
+   write(Table2,file=results2,ncol=1)
+ 
+   Sweave(paste(dir,"spike-in-assessment.Rnw",sep="/"))
+ }
> 
> if(F3){
+   Table2.133 <- rbind(tableAll(spikein.assessment.133),
+                       tableAll(spikein.assessment2.133))
+   
+   results2.133 <- "results2-133.txt"
+   Table2.133 <- rbind(Table2.133,spikein133.ngenes)
+   write(Table2.133,file=results2.133,ncol=1)
+   Sweave(paste(dir,"spike-in-133-assessment.Rnw",sep="/"))
+ }
Writing to file spike-in-133-assessment.tex
Processing code chunks ...
 1 : term hide
 2 : term verbatim
 3 : term verbatim
 4 : term verbatim eps pdf
 5 : term verbatim eps pdf
 6 : term verbatim eps pdf
 7 : term verbatim eps pdf
 8 : term verbatim eps pdf
 9 : term verbatim eps pdf
10 : term verbatim eps pdf
11 : term verbatim eps pdf
12 : term verbatim eps pdf
13 : term verbatim eps pdf
14 : term verbatim eps pdf
15 : term verbatim eps pdf

You can now run LaTeX on spike-in-133-assessment.tex 
> if(F1 | F2){
+   Table <- rbind(Table,spikein.ngenes,dilution.ngenes)
+   results <- "results.txt"
+   write(Table,file=results,ncol=1)
+ }
> proc.time()
[1] 128.03   7.12 142.88   0.00   0.00
>