BI203 dChip for Gene Expression and SNP Microarray Data Analysis

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==Objective==
==Objective==
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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.
==Course outline==
==Course outline==
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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 directory file.
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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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* Session 2: Gene Expression Analysis: Case studies with two groups, gene filtering, group comparison, clustering
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* Session 2: Gene Expression Analysis: Case studies with comparison of two groups, gene filtering and clustering
* Session 3: Gene Expression Analysis: Case studies with ANOVA, correlation, enrichment and classification
* Session 3: Gene Expression Analysis: Case studies with ANOVA, correlation, enrichment and classification
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* Session 4: Gene Expression Analysis: Resampling, manipulating trees, gene function enrichment, pathways, FDR, combine comparisons
* Session 4: Gene Expression Analysis: Resampling, manipulating trees, gene function enrichment, pathways, FDR, combine comparisons
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* Session 5: SNP Genotyping 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 scores from saved text files; use of array list file, sample information file, dChip directory file.
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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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* Session 6: SNP Genotyping Analysis: LOH and copy number analysis with sample data; export.
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* Session 6: SNP Array Analysis: LOH and copy number analysis with sample data; export.
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* Session 7: SNP Genotyping Analysis: Intricacies of CN and LOH analysis, parameters used; GVHD
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* Session 7: SNP Array Analysis: Intricacies of copy number and LOH analysis, parameters used
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* Session 8: SNP Genotyping Analysis: Allele sharing analysis, linkage analysis; automation in dChip
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* Session 8: SNP Array Analysis: Allele sharing analysis, linkage analysis; automation in dChip  
==Instructors==
==Instructors==
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==Course schedule==
==Course schedule==
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Upcoming:
* [http://edu.bioinformatics.org/TAA Course TAA (on-site), January 26-28, 2009, 9:00-17:00 US EST daily (Boston)]
* [http://edu.bioinformatics.org/TAA Course TAA (on-site), January 26-28, 2009, 9:00-17:00 US EST daily (Boston)]
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Completed:
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* [http://edu.bioinformatics.org/CCT Course CCT (online), June 16-20, 2008, 15:30-17:30 GMT daily]
* [http://edu.bioinformatics.org/CCT Course CCT (online), June 16-20, 2008, 15:30-17:30 GMT daily]

Revision as of 19:58, 17 December 2008

Contents

Objective

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.

Course outline

Instructors

Course schedule

Upcoming:

Completed:

Registration

Registration takes two steps. First, if you haven't already done so, 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 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.

Registration deadline: When full

Tuition & discounts

The fee for this course is $995 USD (commercial, government)

Discounted rates are available, as follows:

Logistics

Online courses are offered via an online meeting system. Access information will be provided prior to the start of the course. Each session will last 90 to 120 minutes (total of 8 sessions), 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.

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 Adobe Flash plugin. A microphone and webcam is not required for this course. The necessary software, lecture notes and exercises will be provided.

Certification

This course is certified by the 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.

Additional information

If you have any questions, please send a message to J.W. Bizzaro (login required) or call +1 978 562 4800.

See also

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