Hands on Training on R and Bioconductor for Microarray Data Analysis

Organized By Scientific Bio-Minds, Bangalore

Duration: 15 Days

Timing: 10AM-4PM

Venue: - Scientific Bio-Minds, #165, 4^th Main, 2^nd 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, 4^th Main, 2^nd 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 05^th 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