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Getting started with microarray analysis in R Judith Boer, updated 10/11/08

Getting started with microarray analysis in R

Follow instruction on how to install R and Bioconductor packages from:http://www.bioconductor.org/docs/install-howto.html

The Bioconductor website has links to introductory course material, overview of functions, etc.

One useful site is: http://faculty.ucr.edu/~tgirke/manuals.htm

Download a nice Windows editor for R scripts:http://www.sciviews.org/Tinn-R/ , kiesSetup for Tinn-R, old stable version (1.17.2.4)

First practical: Introduction to RThe instructions for the practical are to be found in Introduction_to_R_Exercises_Nov_2004.pdf.You will need to load the input file exercise1_signal.txt. Some basic R hints and functions can befound inR_basic-functions.r. This file can be opened in Notepad.

Using microarray-related packages in R

To learn to use R for microarray data analysis, practise with the following modules from theMicroarray Analysis Course. Lectures on the same topics are also available:http://www-bioinf.erasmusmc.nl/MGC/

Practical: Normalization in R

Differential gene expression in R

Pathway analysis using the globaltest

For additional scripts see the R user group website:http://chromium.liacs.nl/R_users/

Remember: the learning curve is steep! In the beginning, be prepared for lots of error messagesetc. that are best solved by finding people around you who have some experience in R. At HumanGenetics, these include Peter-Bram 't Hoen, Rene de Menezes, Judith Boer, Maarten vanIterson, and Henk Buermans.

For more information seehttp://www.humgen.nl/MicroarrayAnalysisGroup.html, and sign up forour genomics/bioinformatics seminars (http://www.humgen.nl/genomics-bioinf.html) by mailing toJudith Boer:j.m.boer@lumc.nl

Other coursesRene de Menezes gives a special R course on microarray analysis as well, including morestatistics. This course is given when there are enough people interested. The course material canbe found at http://dial.liacs.nl/Courses/CMSB%20Courses.htmland contains some overlap withpractical modules in the MGC course.

Open source data analysis tools that use R in the backgroundWhile R gives you maximal flexibility, if you want to do mostly standard analyses, there areseveral initiatives that have incorporated R scripts in a user-friendly interface, e.g.http://bioinformatics.skcc.org/webarray/.

Also, there are open source data analysis tools that include many of the options of Spotfire andR, e.g. BRB-ArrayTools at http://linus.nci.nih.gov/~brb/download_3_5_0.htm.

http://www.bioconductor.org/docs/install-howto.htmlhttp://faculty.ucr.edu/~tgirke/manuals.htmhttp://www.sciviews.org/Tinn-R/http://www.sciviews.org/Tinn-R/http://www.sciviews.org/Tinn-R/Tinn-R%201.17.2.4%20setup.exehttp://www.sciviews.org/Tinn-R/Tinn-R%201.17.2.4%20setup.exehttp://www-bioinf.erasmusmc.nl/MGC/monday/011/Introduction%20to%20R%20exercises_2008_short.dochttp://www-bioinf.erasmusmc.nl/MGC/monday/011/exercise1_signal.txthttp://www-bioinf.erasmusmc.nl/MGC/wednesday/031/R_basic-functions_060508.rhttp://www-bioinf.erasmusmc.nl/MGC/wednesday/031/R_basic-functions_060508.rhttp://www-bioinf.erasmusmc.nl/MGC/http://chromium.liacs.nl/R_users/http://chromium.liacs.nl/R_users/http://www.humgen.nl/MicroarrayAnalysisGroup.htmlhttp://www.humgen.nl/MicroarrayAnalysisGroup.htmlhttp://www.humgen.nl/genomics-bioinf.htmlmailto:j.m.boer@lumc.nlhttp://dial.liacs.nl/Courses/CMSB%20Courses.htmlhttp://dial.liacs.nl/Courses/CMSB%20Courses.htmlhttp://bioinformatics.skcc.org/webarray/http://bioinformatics.skcc.org/webarray/http://linus.nci.nih.gov/~brb/download_3_5_0.htmhttp://www.bioconductor.org/docs/install-howto.htmlhttp://faculty.ucr.edu/~tgirke/manuals.htmhttp://www.sciviews.org/Tinn-R/http://www.sciviews.org/Tinn-R/Tinn-R%201.17.2.4%20setup.exehttp://www-bioinf.erasmusmc.nl/MGC/monday/011/Introduction%20to%20R%20exercises_2008_short.dochttp://www-bioinf.erasmusmc.nl/MGC/monday/011/exercise1_signal.txthttp://www-bioinf.erasmusmc.nl/MGC/wednesday/031/R_basic-functions_060508.rhttp://www-bioinf.erasmusmc.nl/MGC/http://chromium.liacs.nl/R_users/http://www.humgen.nl/MicroarrayAnalysisGroup.htmlhttp://www.humgen.nl/genomics-bioinf.htmlmailto:j.m.boer@lumc.nlhttp://dial.liacs.nl/Courses/CMSB%20Courses.htmlhttp://bioinformatics.skcc.org/webarray/http://linus.nci.nih.gov/~brb/download_3_5_0.htm

8/14/2019 Micro Array Analysis Getting Started With R

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Getting started with microarray analysis in R Judith Boer, updated 10/11/08

Judith Boer, Human Genetics, LUMC. Updated 10/11/08