Day 1 Friday 13th June 2008
Morning Session 9am-12.15pm
Welcome to BioInformatics Workshop on R
8.45am-9.00am Registration and Walk-in Payment
  • Guest-of-honour: tbd
  • Welcome to participants from AMBIS Vice-President Olivo Miotto
  • Setting up your laptops
    • 9.00am-10.30am Session I : Surviving R
    Objectives
  • Getting Help in R
  • Importing and Exporting data
  • Manipulating your data
  • Presenting your DATA (Graphics)

    Worksheet for session: Available at Course Materials Webpage
    Presentation slides for session: Available at Course Materials Webpage
    • 10.30am-10.45am Morning /Tea Break with refreshments
    10.45am-12.15pm Session II : Bioconductor-ing
    Objectives
  • Bioconductor packages
  • Familiarising with Expression data class
  • Data Annotation
  • Databases available, GO, biomaRt

    References:
    Gentleman et al (2004) Genome Biology 2004, 5:R80
    "Bioconductor: open software for computational biology and bioinformatics"

    Dataset for session: Available at the Course Materials Webpage
    Worksheet for session: Available at Course Materials Webpage Presentation slides for session: Available at Course Materials Webpage
    • 12.15pm-1.15pm Lunch
    Afternoon Session 1.15pm-5.30pm
    Welcome to the hands-on session of the BioInformatics Workshop on BioConductor
    1.15pm-3.00pm Session III : Real World Dataset ( Chang Breast Cancer Paper)
    Objectives
  • Preprocessing
  • Heatmaps and Clustering
  • PCA Analysis
  • Differential Gene Expression Analysis
  • ROC curves

    References: Chang et al. (2003) | From Elsevier | From Lancet | Via NUS |

    Lancet 2003, 362:362-369
    "Gene Expression profiling for the prediction of therapeutic response to docetaxel in patients with breast cancer"

    Dataset for session: Available at the Course Materials Webpage
    Worksheet for session: Available at Course Materials Webpage
    • 3.00pm-3.15pm Afternoon Coffee/Tea Break with refreshments
    3.15pm-5.00pm Session IV: Real World Dataset (CNV/SNP analysis)
    Objectives
  • Finding Breakpoints
  • Simple SNP studies

    References:
    tba
    Worksheet for session: Available at Course Materials Webpage
    • 5.00pm-5.30pm Discussion
    5.30pm-5.45pm Farewell and Certificate Presentation