Organized By Scientific Bio-Minds, Bangalore
Duration:
15 Days
Timing: 10AM-4PM
Venue: -
Scientific Bio-Minds, #165, 4th Main, 2nd
B Cross, Talakavery Layout, Near Vishwa Amrutha Apartment, Amruthahalli,
Sahakarnagar Post, Bangalore-560092
Objective of the Program
This
training will show you how to use the BioConductor package in R to analyze
Affymetrix microarray data. You will learn to:
·
Import
your own or publicly available microarray data
·
Assess
and control the quality of the data
·
Identify
differentially expressed genes between two or more groups of samples
·
Determine
which Gene Ontology categories are over-represented in the set of
differentially expressed genes
·
Group
genes with similar expression profiles
Summary
This
training is aimed at researchers who are applying or planning to use Affymetrix
microarrays in their research. The aim of this training is to familiarise the
participants with microarray data analysis methodologies and provide hands-on
training on the use of BioConductor for Affymetrix microarray analysis.
Participants can use their own data during the training as long as the design
of the experiment is similar to those used in the training e.g. comparison of
two or multiple groups of samples.
Prerequisite
Depending
on the number of participants (max 20), it is possible that you have to share
the laptop with one other participant but you can also choose to bring your own
laptop for this training session.
Syllabus
1.
General
Introduction to R – what is R, console and Rstudio
2.
Introduction
to R – handling the environment and data types
3.
Introduction
to R – data input/output and basic scripting
4.
Learn
R flow control and data structures
5.
Use
vectorized calculations
6.
Write
R functions
7.
Understand
basic R graphics
8.
Introduction
to genomics and microarray technology
9.
Introduction
to statistics and microarray analysis
- Summary statistics and exploratory data
analysis methods
- Clustering: partitioning and hierarchical
methods
- Sources of variability and experimental
design
- Data preprocessing for expression arrays
1.
Hypothesis
testing and Linear Models
- Two-sample statistics
- Introduction to linear models for factorial
experiments
- Multiple testing issues
2.
Classification
I
- Linear methods for classification
- Linear discriminant analysis and variations
- Logistic regression
3.
Classification
II
- Tree-based methods
- Ensembles: bagging, boosting, random
forests
4.
Classification
III
- Support vector machines
- Neural networks
5.
Model
selection
- Bias, variance and model complexity
- Model search (forward/backwards/stochastic)
- Model selection criteria: AIC/BIC
- Cross validation and performance assessment
- Application to estimating the number of
clusters
6.
Regression
- Penalization and selection
- Continuous and survival endpoints
7.
Hidden
markov models & Functional annotation
- HMM, GHMM, paired
HMM and their applications in genomics
- Functional annotation and motif finding for
groups of co-expressed genes
8. Quality control and
preprocessing of Affymetrix arrays introduction
Talks and Presentations: - Scientific Bio-Minds Team members
Who may participate in this
workshop?
Researchers,
Scientists, Research Scholars and Students of:
·
Any
stream of Life Sciences/Medicine with needs for large-scale biological (tera
and peta-scale) data analysis and interpretation
·
Computer
Science interested in learning big data tools and technologies for large-scale
biological data
Registration fees:
|
|
Fees
|
|
Industry/
Corporate
|
Rs
8500/-
|
|
Govt/
Faculty
|
Rs
7500/-
|
|
Graduate/
Post-graduate/ PhD students
|
Rs
6000/-
|
Mode
of payment:
·
Registration
fee should be sent through DD/Cheque in favor of ‘Scientific Bio-Minds,
Bangalore', payable at Bangalore along with the completely filled registration
form.
·
Details
of Bank Account for transfer of Funds through NEFT
·
DD/Cheque
should reach by January 05, 2015 to the following address:
Scientific Bio-Minds,
#165, 4th Main, 2nd B Cross, Talakavery layout,
Near Vishwa Amrutha
Apartment, Amruthahalli, Sahakarnagar Post,
Bangalore-560092,
Karnataka, India
Participants
are requested to make their own arrangements for transportation and
accommodation.
Deadline
for registration:
Kindly register for the event on or before 05th January 2015. The
seats are limited; an early registration will help us to confirm your participation.
For further information, contact:
Dr.C.N.Prashantha,
Mobile: - +91-9844158444
