BI203 dChip for Gene Expression and SNP Microarray Data Analysis

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==Objective==
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==Objectives==
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This course will teach the workings of the [http://biosun1.harvard.edu/complab/dchip/ dChip application] for Gene Expression and SNP Genotyping analysis. We will cover topics such as importing arrays, performing normalization, model based expression calculations, gene and SNP filtering, clustering, linkage and LOH analysis, and much more.
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This course will teach the workings of the [http://biosun1.harvard.edu/complab/dchip/ dChip application] and cover topics such as importing arrays, performing normalization, model based expression calculations, gene and SNP filtering, clustering, linkage, LOH and copy number analysis.
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==Course outline==
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* Session 1: Preparing to import CEL files for gene expression analysis, with basic actions such as normalization and model-based expression index calculations. Re-importing saved "DCP" files and importing expression indices from saved text files
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* Session 2: Gene expression case studies with two groups, gene filtering, group comparison, clustering
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* Session 3: Same as session 1, except with SNP genotyping data
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* Session 4: LOH and copy number analysis with sample data
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* Sessions 5-6: Advanced case studies in gene expression analysis, with Cheng Li
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* Sessions 7-8: Advanced case studies in SNP genotyping analysis, with Cheng Li
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==Instructors==
==Instructors==
* [http://www.hsph.harvard.edu/~cli/ Prof. Cheng Li], Dana Farber Cancer Institute and Harvard School of Public Health, author of dChip
* [http://www.hsph.harvard.edu/~cli/ Prof. Cheng Li], Dana Farber Cancer Institute and Harvard School of Public Health, author of dChip
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* [[Shailender Nagpal]], Bioinformatics Organization and Tanisha Systems
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* [[Shailender Nagpal]]
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==Course schedule==
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* [http://edu.bioinformatics.org/CCT Course CCT (online), May 19-23, 2008]
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==Registration==
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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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Registration deadline: When full
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==Tuition & discounts==
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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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==Syllabus==
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* Academic and non-profit research organizations, $597
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* Students paying for themselves (not getting reimbursement) and unemployed individuals (verification required), $298
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* [[Membership|Professional members]] get an additional 20% discount.
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* Limited scholarships may also be available for those in low-income economies.
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==Logistics==
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* Session 1: Gene Expression Analysis: Preparing to import CEL and CHP exported txt files, with basic actions such as normalization and model-based expression index calculations. Re-importing saved "DCP" files and importing expression indices from saved text files. Use of array list file, sample information file, dChip data file list.
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Online courses are offered via an online meeting system.  Access information will be provided prior to the start of the course. Each lecture will last 90 to 120 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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* Session 2: Gene Expression Analysis: Case studies with comparison of two groups, gene filtering and clustering
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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].  A microphone and webcam is not required for this course.  The necessary software, lecture notes and exercises will be provided.
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* Session 3: Gene Expression Analysis: Case studies with ANOVA, correlation, enrichment and classification
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==Certification==
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* Session 4: Gene Expression Analysis: Resampling, manipulating trees, gene function enrichment, pathways, FDR, combine comparisons
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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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* Session 5: SNP Array Analysis: Preparing to import CEL and CHP exported txt files, with basic actions such as normalization and model-based expression index calculations for copy number analysis; re-importing saved "DCP" files and importing genotypes and SNP signals from saved text files; use of array list file and sample information file.
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==Additional information==
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* Session 6: SNP Array Analysis: LOH and copy number analysis with sample data; export.
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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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* Session 7: SNP Array Analysis: Intricacies of copy number and LOH analysis, parameters used
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==See also==
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* Session 8: SNP Array Analysis: Allele sharing analysis, linkage analysis; automation in dChip
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* [[BI201A Gene Expression Analysis]]
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{{Course footer
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* [[BI201B SNP Genotyping]]
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|hours=6
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* [[Educational services|Educational services at Bioinformatics.Org]]
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}}

Latest revision as of 20:22, 19 May 2011

Contents

Objectives

This course will teach the workings of the dChip application and cover topics such as importing arrays, performing normalization, model based expression calculations, gene and SNP filtering, clustering, linkage, LOH and copy number analysis.

Instructors

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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