BI201 Gene Expression Analysis

This course helps to demystify Affymetrix analysis so that any researcher can take the basic steps to go from a chip image to a list of genes that are up- or down-regulated in an experiment. Various tools will be covered, e.g. Affymetrix Expression Console (replacing GCOS), Microsoft Excel, MathWorks MATLAB, and free tools like R/Bioconductor and dChip. It is geared towards researchers who conduct microarray experiments to study genome-wide expression changes and understand the underlying mechanisms of gene regulation in samples of interest.

Most scientists are not able to analyze the resulting data themselves, and they are not able to get desired results using traditional tools like Microsoft Word and Excel or with advanced software provided by commercial vendors. The freeware solutions come either with a steep learning curve or as black-box interfaces that provide limited functionality with little or no technical support. In the midst of all this is the fundamental lack of understanding among scientists on how the technology works and what the fundamental parts of the analysis are.

No experience is required, although prior experience with any other programming language will be helpful. Math skills will also be useful.

Sessions 1 & 2

Introduction to Expression Console -- the environment, creating and saving experiments, importing and exporting data, normalization settings, from DAT->CEL->CHP->RPT files and their significance, importing and exporting data

Sessions 3 & 4

dChip software: importing expression data and annotation information into dChip, normalization, gene filtering, clustering, visualization along chromosome, gene ranking by confidence intervals and pvalues for group studies, exporting to Excel

Sessions 5 & 6

R/Bioconductor: installing and configuring bioconductor for gene expression analysis, obtaining normalized gene expression scores, performing statistics to obtaining differentially regulated genes in time series or group studies

Sessions 7 & 8

MATLAB: importing expression data in MATLAB, thresholding, normalization, gene filtering, clustering, classification, statistical gene ranking for time series and group studies, exporting to excel, building custom user interfaces for advanced applications.

This course is taught by Shailender Nagpal, M.S.

Registration

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Step 1

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Step 2

Register for this course by sending in the registration form (PDF; use this form if paying by US checks, credit card or corporate purchase order).

On-demand course held on-line

This course might be taught on-demand, on-line. Please check the list of on-demand courses to see if this course can be taken as such.

An on-demand version provides pre-recorded video lectures. Once registered, you may begin by viewing the first lecture video, and if you have any questions, you may then email the instructor.

Slides are available with both on-demand and live of courses, and many also have examples (such as data and scripts). Assignments are also provided for your edification but are not graded. And, when finished, you may request a certificate of attendance.

On-demand course tuition:

• For-profit & government: $600 USD
• Non-profit & self-pay: $400 USD
• See below for additional discounts.

Students who've taken the on-demand version of this course can access the course page here.

Live course held online

This course might also be taught live, on-line. Please check the calendar to see if it will be held in the near future.

Live, online course tuition:

• For-profit & government: $1,000 USD
• Non-profit & self-pay: $600 USD
• See below for additional discounts.

Registration deadline: When full

Students who've taken the live course can continue to access their course pages here. (Access to completed courses is available to enrolled students only, because of privacy and confidentiality issues.)

Live course held on-site

We can come to your facility to teach this course. Please contact us for additional information.

Discounts

Additional discounts are available as follows:

• Professional members: 20% discount
• Limited scholarships may also be available for those residing in low-income economies (please inquire).

Certification

This course is certified by Bioinformatics.org, one of the oldest and largest international affiliations in the field, and it will count as 6 "Continuing Scientific Education" (CSE) units (one unit per contact hour) within Bioinformatics.org. Students completing the course will receive a certificate attesting to that.

Refund policy

For any course type, if a student is not satisfied with the conduct or content of a course, they may request a full refund within the first two days of lecture. After two days but within a week, a 50% refund will be granted. After one week, a 100% credit toward another course will be granted. No refunds or credits apply beyond those stated here.

Additional information

Please contact us for questions or additional information.

See also

• Educational services at Bioinformatics.org