=========================================================================== Annotated schedule ===========================================================================

R/Bioconductor Short Course on the Analysis of DNA Microarray Data Robert Gentleman and Sandrine Dudoit December 4-6, 2002

Each session is 90 minutes, 15 min break between sessions.

Wednesday, December 4th =======================

AM 9:00-12:15

• Introduction to genome biology
• Introduction to DNA microarray technologies: spotted DNA microarrays and Affymetrix oligonucleotide chips

PM 14:00-17:15

• Pre-processing DNA microarray data: spotted DNA microarrays and Affymetrix oligonucleotide chips
• LAB R and Bioconductor basics

overview of Bioconductor project (resources on the Bioconductor website) R and R package system how to install Bioconductor packages help vignettes (functions to manage and use vignettes) OOP, Biobase exprSet basic data structures and functions

Can build on slides from JAX lectures III and IV (p. 1-11), but need to add slides on installation and vignettes. Also need basic R slides.

Thursday, December 5th ======================

AM 9:00-12:15

• Using Bioconductor packages
• LAB Using Bioconductor packages

more on Biobase annotate (data packages) geneplotter differential expression: genefilter, multtest, edd

Can use Hopkins lect V (p. 1-65) but needs to be reorganized and need to add new Bioconductor functions

PM 13:15-14:45

• LAB Bioconductor packages for pre-processing DNA microarray data: spotted DNA microarrays and Affymetrix oligonucleotide chips

Hopefully can use vExplorer

Friday, December 6th ====================

AM 9:00-12:15

• Distances, cluster analysis (unsupervised learning)
• LAB Distances, cluster analysis

PM 14:00-17:15

• Feature selection, classification (supervised learning)
• LAB Feature selection, classification

We can use some of the materials from summer course and Hopkins lect V, but still needs lots of work, especially for lab.

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Notes on material to cover in the labs ======================================

R and Bioconductor basics -------------------------

Resources: CRAN, manuals install R help.start(), demo(), example() packages: how to install, load (library()) ls, search basic data structures How to install BioC packages (Windows , Linux): reposTools, getBioC Vignettes: vExplorer OOP: exprSet, phenoData, basic methods. ...

Using Bioconductor packages -------------------------- data packages (get, ls) annotate: genbank locuslinkByID, locuslinkQuery pubmed getPMInfo (works on xmlDocument) pubMedAbst (absText, abstUrl, articleTitle, authors, journal, pubDate) buildPubMedAbst pm.getabst, pm.abstGrep, pm.titles (on pubMedAbst class) geneplotter genefilter multtest edd ll.htmlreport

Pre-processing --------------

affy marray

use vExplorer, demo

Classification and clustering -----------------------------

distance functions plotcorr mds pam hclust cophenetic