BI201 Gene Expression Analysis

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==Objective==
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==Objectives==
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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. GCOS, Excel, MATLAB, and free tools like R 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. 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.  
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This course helps to demystify [http://www.affymetrix.com/products/index.affx 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. [http://www.affymetrix.com/products/software/specific/expression_console_software.affx Affymetrix Expression Console] (replacing [http://www.affymetrix.com/products/software/specific/gcos.affx GCOS]), Microsoft Excel, [http://www.mathworks.com/products/matlab/ MathWorks MATLAB], and free tools like [http://www.r-project.org/ R]/[http://www.bioconductor.org/ Bioconductor] and [http://www.biostat.harvard.edu/complab/dchip/ 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.  
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No experience is required, although prior experience with any other programming language will be helpful. Math skills will also be useful. This course is certified by the [[Bioinformatics Organization|Bioinformatics Organization, Inc.]], the largest international affiliation in the field, and it will count as '''10''' "Continuing Scientific Education" (CSE) credits (one credit per contact hour) within the Organization. Students completing the course will receive a certificate attesting to that.
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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.  
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==Course outline==
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No experience is required, although prior experience with any other programming language will be helpful. Math skills will also be useful.
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* Day 1: Introduction to GCOS – 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
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==Instructor==
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* Day 2: 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.
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* Day 3: 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.
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* Day 4: 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.
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* Day 5: Problem solving session involving some real gene expression data
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==Course schedule==
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* [[Shailender Nagpal]]
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This course has been offered several times. Access to completed courses is available to enrolled students only, because of privacy and confidentiality issues. If you are interested in an upcoming course, register using instructions below.
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==Syllabus==
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* [http://edu.bioinformatics.org/ATT Course ATT (online), Feb 18-22, 2008]
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* Session 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
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* [http://edu.bioinformatics.org/AGG Course AGG (online), December 17-21, 2007]
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* [http://edu.bioinformatics.org/GT/site Course GT (online), July 23-28, 2007]
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* [http://edu.bioinformatics.org/AK/site Course AK (online), February 26 - March 2, 2007]
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* [http://edu.bioinformatics.org/BI201A Site license login]
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==Registration==
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* Session 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.
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Registration comprises of two steps. First, [https://edu.bioinformatics.org/login/signup.php create an online account] to access the educational section of our website. Second, register for this course by making a payment using either the online registration form (click on the scheduled course above; ''use this form only for credit card payments via secured PayPal''), or by sending in the [http://edu.bioinformatics.org/download/registration_form.pdf Mail-in registration form] (~150 kB PDF, ''use this form if paying by US checks, credit card or corporate purchase order''). Please check the tuition rates and discounts below.
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* Session 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.  
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Registration deadline: When full
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* Session 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.
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==Tuition and Discounts==
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{{Course footer
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|hours=6
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The fee for this course is $895 USD (Commercial, Government)
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Discounted rates are available, as follows:
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* Academic and non-profit research organizations, $597 (USD)
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* Students paying for themselves (not getting reimbursement) and unemployed individuals (verification required), $298
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* Limited scholarships may also be available
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* Professional members get an additional 20% discount
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==Logistics==
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http://edu.bioinformatics.org/images/asap_logo.png
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Online courses are offered on the ASAP online meeting system.  Access information will be provided prior to the start of the course. Each lecture will last 45 to 90 minutes, depending on the topics covered. For those who cannot attend the lectures at those times, the lectures will be recorded and placed on the course website as Flash videos (resolution reduced by 30%) each day, within one day.  Students will also be able to communicate with the instructor and other students via the course forums.  Lecture attendance is therefore not required.
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Since this will be an interactive, hands-on workshop, all attendees will need a computer with a broadband Internet connection (1 Mbps or faster is strongly recommended for those watching the live lecture), a sound card with speakers, a modern Web browser, and the [http://www.adobe.com/products/flashplayer/ Adobe Flash plugin].  Please [[ASAP requirements|check the specific system requirements for your computer]].  A microphone and webcam is not required for this course.  The necessary software, lecture notes and exercises will be provided.
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<div style="border-top: solid 1px black; font-size: small; margin: 3em 0em 0em 1em; width: 20em;">
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''ASAP is a trademark of Convoq, Inc.<br />Other names are trademarks of their respective owners.''
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</div>
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==Additional information==
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If you have any questions, please send a message to [http://edu.bioinformatics.org/message/discussion.php?id=100003 J.W. Bizzaro] (login required) or call +1 978 562 4800.
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==See also==
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* [[Educational services|Educational services at Bioinformatics.Org]]
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Latest revision as of 07:48, 10 February 2012

Contents

Objectives

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.

Instructor

Syllabus

Scheduled courses

If you are interested in an upcoming course, register using instructions below. (Access to completed courses is available to enrolled students only, because of privacy and confidentiality issues.)

Registration

Registration for courses at Bioinformatics.Org takes two steps:

Step 1
If you haven't already done so, create an on-line account to access the educational section of our website. Please note that the registration for our educational system is separate from that of the main website; you will require another account.
Step 2
Register for the course by making a payment using either the on-line registration form (click on the name of the course where it appears in the list of upcoming courses; use this form only for PayPal payments and credit card payments via secured PayPal), or by sending in the registration form (PDF; use this form if paying by US checks, credit card or corporate purchase order).

Please also check the course tuition rates and discounts.

Registration deadline: When full

Tuition & discounts

Live instruction held on-line
Live instruction held on-site
On-demand instruction held on-line

Additional discounts are available as follows:

Logistics

The necessary software, lecture notes and exercises will be provided.

Live instruction held on-line

On-line/live courses use the WebEx on-line meeting system. Access information will be provided prior to the start of the course. Unless otherwise noted, each lecture begins at 16:00 GMT and runs for about two hours, depending on the topics covered.

For those who cannot attend the lectures at those times, the lectures will be recorded and placed on the course website as AVI video files each day, within one day. Students will also be able to communicate with the instructor and other students via the course forums. Lecture attendance is therefore not required.

Since this will be an interactive, hands-on workshop, all attendees will need a computer with a broadband Internet connection (1 Mbps or faster is strongly recommended for those watching the live lecture), a sound card with speakers, a modern Web browser, and Java. A microphone and webcam are not required but may be used.

Certification

This course is certified by the Bioinformatics Organization, Inc., the largest international affiliation in the field, and it will count as 6 "Continuing Scientific Education" (CSE) units (one unit per contact hour) within the Organization. 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

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