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Day 1 Friday 13th June 2008
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Morning Session 9am-12.15pm
Welcome to BioInformatics Workshop on R
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8.45am-9.00am
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Registration and Walk-in Payment
Guest-of-honour: tbd
Welcome to participants from AMBIS Vice-President Olivo Miotto
Setting up your laptops
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9.00am-10.30am
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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
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10.30am-10.45am
Morning /Tea Break with refreshments
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10.45am-12.15pm
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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
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12.15pm-1.15pm Lunch
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Afternoon Session 1.15pm-5.30pm
Welcome to the hands-on session of the
BioInformatics Workshop on BioConductor
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1.15pm-3.00pm
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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
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3.00pm-3.15pm
Afternoon Coffee/Tea Break with refreshments
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3.15pm-5.00pm
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Session IV: Real World Dataset (CNV/SNP analysis)
Objectives
Finding Breakpoints
Simple SNP studies
References:
tba
Worksheet for session:
Available at Course Materials Webpage
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5.00pm-5.30pm
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Discussion
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5.30pm-5.45pm Farewell and Certificate Presentation
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