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Course page: Basic Introduction to R (6-7 Oct) Workshop schedule here. Slides from the workshop: Laurent Gautier - annotation tutorial Laruent Gautier - microarrays tutorial Benilton Carvalho - dealing with SNP and CN data Benilton Carvalho - expression tutorial ******** Tools for Thursday and Friday Scripts:
Additional packages to be used Thursday and Friday. The code:
pkgs <- c("maqcExpression4plex", "genefilter", "geneplotter", "limma", "RColorBrewer")
****** IMPORTANT Information regarding hard-/software: Computer recommendations Your laptop should have- an operating system: any of Linux, Microsoft Windows, Mac OSX R -- preferably R-2.7.2. installed. It is recommended that R-2.7.2. is installed on your computer prior to the introductory course and the workshop. R-2.7.2. can be downloaded for free. Go to the R Project home page. Then, select CRAN (short for The Comprehensive R Archive Network) in the left menu which will bring you the CRAN mirrors. Enter any of the Scandinavian mirrors -> select your platform and follow the instructions on the screen. BioConductor packages - code to run in the R console: -- Highly recommended, but optional code to run in R before the workshop -- This will download and install a number of packages from the bioconductor website onto the computer you will bring to the workshop. Downloading and installing will still be possible on the day, but time consuming. # Laurent Gautier - 2008 # The code: packs <- c("ALL", "AnnotationDbi", "Biostrings", "Biobase", Additional BioConductor packages (step 1 and 2) 1. Benilton Carvalho anticipates the following packages to be used during the exercises "VanillaICE", "SNPchip", "pd.genomewidesnp.6". As the last pack is substantial in size, we advise download and installation prior to the course. You can use the same command as above. In other words, in R run this code: packs <- c("SNPchip", "VanillaICE", "pd.genomewidesnp.6") source("http://www.bioconductor.org/biocLite.R")
2. Download and install "aroma.affymetrix" by running the following code: source("http://www.braju.com/R/hbLite.R")
3. Download and install "hapmapsnp6" by running the following code in R: (NEW) source("http://www.bioconductor.org/biocLite.R") biocLite("hapmapsnp6")
Don't worry if you are having difficulties downloading and installing these items. Highly skilled persons will be happy to help during the workshop. Go to:
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