R version 2.10.1 (2009-12-14) Copyright (C) 2009 The R Foundation for Statistical Computing ISBN 3-900051-07-0 R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(affycompData, lib.loc="/home/hjaffee/Rlibs.AFFY3") Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. > library(affycomp, lib.loc="/home/hjaffee/Rlibs.AFFY3") > library(tools) > > 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). > > # HJ Feb 23, 2010 > ## make/save assessments (used to be in save_assessments.R) > > dir.create("data") > 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) + save(dilution.assessment,file="data/dilution.assessment.rda",compress=TRUE) + # 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) + save(spikein.assessment,file="data/spikein.assessment.rda",compress=TRUE) + 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) + save(spikein.assessment2,file="data/spikein.assessment2.rda",compress=TRUE) + spikein.ngenes <- nrow(exprs(s)) + } Performing 6 assessments that will take a few minutes...... Using only a subset of the spike in data Performing 3 assessments that will take a few seconds... > > f <- "hgu133.csv" > if(file.exists(f)){ + s <- read.spikein(f,"hgu133a") + spikein.assessment.133 <- + assessSpikeIn(s,verbose=verbose,method.name=method.name) + save(spikein.assessment.133,file="data/spikein.assessment.133.rda",compress=TRUE) + spikein.assessment2.133 <- + assessSpikeIn2(s,verbose=verbose,method.name=method.name) + save(spikein.assessment2.133,file="data/spikein.assessment2.133.rda",compress=TRUE) + spikein133.ngenes <- nrow(exprs(s)) + } Performing 6 assessments that will take a few minutes...... Performing 3 assessments that will take a few seconds... > ## end of make/save assessments > > # 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="/")) + } Writing to file comparison.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 'comparison.tex' Writing to file simple.tex Processing code chunks ... 1 : term hide 2 : term verbatim 3 : echo 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 You can now run LaTeX on 'simple.tex' Writing to file complete-assessment.tex Processing code chunks ... 1 : term hide 2 : term verbatim 3 : term verbatim 4 : term verbatim 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 16 : term verbatim eps pdf 17 : term verbatim eps pdf 18 : term verbatim eps pdf 19 : term verbatim eps pdf You can now run LaTeX on 'complete-assessment.tex' > > if(F1 & !F2){ + Table[1:6,] <- tableAll(dilution.assessment) + + Sweave(paste(dir,"dilution-assessment.Rnw",sep="/")) + } > > 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() user system elapsed 62.80 0.68 63.49