R version has been released on (Linux source code versions)

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1 Installation of R and Bioconductor R is a free software environment for statistical computing and graphics. It is based on the statistical computer language S. It is famous for its wide set of statistical and graphics tools and was recently much extended for bioinformatics analysis (e.g. BioConductor project). R is available for many different platforms (e.g. Windows, Mac, Linux). Hundreds of packages are available via the CRAN depository web site. It compiles and runs on a wide variety of UNIX platforms, Windows and MacOS. Binaries for Windows are also available. To download R, choose the CRAN mirror nearest to you to minimize network load. R version has been released on (Linux source code versions) 1. Downloading R for Windows German CRAN mirror: Click on the left navigation links on "R binaries" Click on the "Index of /bin" folders on "windows/" From here you can download the base package (base) and additional packages (contrib). Click on the "base" link. Download R win32.exe Download and view README.R-2.7.1, CHANGES, NEWS. Download MD5sum file md5sum.txt. 2. Checking the MD5 hash for uncorrupted file status For checking the installation file not to be corrupt, download md5sum.txt, containing a checksum (MD5 Hash) calculated from the bytes of the file. Download MD5summer Beta version a) Place md5sum.txt and R win32.exe into the same directory. b) Unzip md5v12011.zip and start md5summer.exe by clicking on it. c) At "Please select the root folder" choose the folder created in step a. d) Click on the "Verify sums" tab e) At "Open md5sum file" choose the file "md5sum.txt" and click "Open" tab f) Notice the correct check of the MD5 hash and close the program If the program was corrupt, load it down again. R BioConductor Installation Jul

2 3. Installation of R for Windows Install the R program using R win32.exe as administrator. The program should be installed to folder "C:\Programme\R\R-2.7.1". A previous installation need not to be removed. The installation procedure should generate a path variable entry and a link on the desktop. During the installation it may be useful to select at the "User defined installation options" as additional material "Technical Manuals" and "PDF help pages (reference manual)". Display mode: "MDI" (one large window) Help style: "HTML File" Check the Windows path variable for a correct entry and add it eventually manually: Add at "Control Panel" "System" "Advanced" lower tab "Environment variables" lower window system variable Path "Edit" Add at end of line a semicolon ; and C: \Program Files\R\R-2.7.1\bin. Ckick "ok" and restart the PC. Inside the folder "C:\Programme\R\R-2.7.1" there is the main Windows Graphical User Interface Rgui.exe and the Scripting interface Rterm.exe. A desktop link should aim to Rgui.exe. Hint:.Rdata files in a project folder R will also associate files called.rdata with the Rgui program. This files contain an R environment containing all R objects produced during a R usage session. To organize projects it is best to place your data in a specific folder and start R from this folder. After you close R a.rdata file is saved. When you go ojn next time, just click on.rdata to restart the project reloading all packages and data automatically. To start the program double click the R desktop symbol to open Rgui. At menu item "File" "Change dir " "Change working directory to:" you can change the working directory to a place were the.rdata file should be stored. To inspect the documentation and help files select at the menu item "Help" "Console" will show a help window how to use the R console "Html Help" (entry point to all help pages and package-specific help ("Packages") "Manuals (in PDF)" (Manuals for base package) Hint: For a first feeling just go through the "An Introduction to R" manual "Search Help" (for searching help files containing a specified word in the title) For viewing the content of the basic statistics package stats type in Rgui: R BioConductor Installation Jul

3 library(help="stats") help(stats) # The library documentation summary # The help documents partitioned in two trees "Package stats: R Objects" and "Package stats: Titles" Expansion of the title tree allows reviewing single functions. To view the attached packages try sessioninfo(): sessioninfo() 4. Installation of additional packages: Example Sudoku Start Rgui by double clicking the "R 2.7.1" desktop link. For installing a package choose menu item "Packages" "Install Package(s)" Choose a nearby CRAN mirror and in the next window choose the package to install. E.g. try "sudoku". After installation load the package sudoku by typing: library(sudoku) View the help files using help.search("sudoku") Generate a sudoku "sdk1" with 45 blanks and show it: sdk1 <- generatesudoku(nblank=45) sdk1 Play the Sudoku: playsudoku(sdk1) Just close the graphics window to stop playing. Create a working directory using Windows Explorer (e.g. "I:\sdk") and choose it: Select menu item "File" "Change dir " and select "I:\sdk" Make a pdf file from the sudoku: pdf(file = "sdk1.pdf", pointsize = 10) playsudoku(sdk1) dev.off() R BioConductor Installation Jul

4 5. Installation of BioConductor BioConductor is an ensemble of R packages designed for bioinformatic and statistical analysis of biological data produced by functional genomics, originally for microarray data. The actual release is BioC 2.2: Visit the BioConductor website and follow the installation instructions: Use the bioclite.r script from the internet to install it typing into Rgui: Lines with comments start with "#" # Set the website for the installation scripts source(" # install the BioConductor light package bioclite() # install the BioConductor full package getbioc() For working with our Arabidopsis thaliana example data obtained with the Affymetrix ATH1 gene chip and for the usage of extended graphical features additional packages are recommended. These additional packages can also be installed using the bioclite script: bioclite(c("simpleaffy")) # Simple affymetrix analysis bioclite(c("gplots")) # e.g. for greenred color vectors # Loading chip data bioclite(c("ath db")) # NCBI annotation data bioclite(c("ath ")) # NCBI annotation data bioclite(c("ath cdf")) # NCBI chip data bioclite(c("ath probe")) # probe data and sequences Hint: All downloaded packages are temporarily stored in a folder in your user directory: "C:\Documents and Settings\bioinfo\Local Settings\Temp\RtmpF0bjsb\downloaded_packages" You can copy them from there for storage or later offline installation on another computer with a slow internet connection. You can find the packages at the installation folder "\install\r\packages". When installing a package from these zip files use the menu item: "Packages" "Install package(s) from local ZIP file(s)". R BioConductor Installation Jul

5 At the end of the installation site, there is a link to the "BioC Release Packages": Here an overview of "Software" (packages), "AnnotationData" (chips) and "ExperimentData" (example datasets) are provided. You can download any of these data using bioclite() from Rgui. After loading one of the BioConductor packages, e.g.: library(affy) The BioConductor Help system is installed and displayed in a new menu item "Vignettes". The submenu item "base" contains help concerning the BioConductor base packages, the submenu item "affy" help concerning the attached BioConductor package, here affy. It is always possible to search also the R packages folders for pdf files. E.g "C:\Programme\R\R-2.6.1\library\Biobase\doc" contains the pdf files shown in the "Vignettes" "base" submenu. For an overview of attached packages again call sessioninfo: sessioninfo() 6. Usage of Scripts in Rgui If you write longer scripts in Rgui you may want to copy them and save them in a script file. To write from the beginning of a session in a script file open the Rgui script editor: Menu item "File" "New script" and save the script at a convenient position ("Save as ". Type script lines and label one or several lines and than press the two keys "Ctrl+R" to run the script line or block inside Rgui. The saved script can be loaded again using the menu item "File" "Open script", labelled and send to Rgui by pressing the two keys "Ctrl-R". Hint: If you place the script editor window and the Rgui window tiled, you can just use the editor window for typing and send the typed or more lines (labeled) to the Rgui window to become executed. R BioConductor Installation Jul

6 5. Usage of a script file for starting up Rgui Sometimes you want to start a R session with a specific set of commands preloaded, e.g. for playing a sudoku or running a specific type of analysis. If you have to interact with R this can be done with Rgui.exe, else you can use Rterm.exe. I do this for Rgui by placing a cmd batch e.g. "sudoku.bat" and the R startup script file ".Rprofile" into a specific directory, eg. "\sdk". The commands in.rprofile are executed during startup of R from this directory by the batch command file "sudoku.bat" file. Hint: It may not be possible to make a file.rprofile with a leading dot using the Windows notepad, because Microsoft tries to block the user from using in their eyes weird file names. However the editor Proton (see Perl Installation) will do the job. You can save a file with notepad using another name like "Rprofile.txt" and rename it without problems using the cmd.exe terminal: Click on task bar "Start" "Run" type "cmd" Change to the directory with the files by typing e.g. cd "I:\sdk" Rename the file and type: rename Rprofile.txt.Rprofile sudoku.bat cd F:\sdk Rgui --no-restore --no-save Double-clicking sudoku.bat will change the cmd directory and start Rgui using the startup commands found in ".Rprofile". The options of Rgui can be viewed by typing "Rgui -h" in a cmd window. The startup arguments --no-restore will not load a previously present data environment ".Rdata", the option --no-save will not save one during leaving the program..rprofile cat("\n Welcome to R!\n\n") cat("\n Playing Sudoku!\n\n") require(graphics) require(grdevices) require(sudoku) sdk1 <- generatesudoku(nblank=45) playsudoku(sdk1) Since the standard packages are not loaded during executing the startup script, the needed packages have to be loaded by require(package) beforehand. The R BioConductor Installation Jul

7 function cat() for printing something on the screen ("\n" is a line break) is already available, since the necessary package base is always preloaded. 6. Using a script file with Rterm for batch processing If you have a task, where you have an input (like a value table) and an output (like a pdf file of a histogram of the values) and you need not to interact with R (batch processing) you can use Rterm.exe, a file holding R commands and a e.g. "histo.bat" file to run the procedure. The example file "cusp.txt" in folder "\R_data\histo" holds the results of an EMBOSS codon usage analysis of a set of secreted proteins. High values may be proteins highly expressed and strictly adapted to optimal codon usage, low values are perhaps not expressed at all. The batch file may read: histo.bat Rterm --no-restore --no-save -q < R_histo.txt The option "-q" quits R after running. The option "< R_histo.txt" inputs (<) the commands from R_histo.txt The script file may read: R_histo.txt # do not show text on the Rterm window options(echo = FALSE) # Load the package graphics library(graphics) # scan the data of the file cusp.txt into the vector x x <- scan("cusp.txt") # open the printing device pdf for a specified file and using a character point size pdf(file = "cusp_hist.pdf", pointsize = 10) # calculate breaks at every 5th position, x-axis from -400 to 450, title (main) hist(x, breaks = (max(x)-min(x))/5, xlim = c(-400,400), main = "Histogram of data in neg2.txt") # close the pdf printer device dev.off() # quit the R program q() Clicking on histo.bat will execute the script and produces a pdf-file showing the histogram. R BioConductor Installation Jul