BI201C dChip for Gene Expression and SNP Microarray Data Analysis

From Bioinformatics.Org Wiki

Jump to: navigation, search

Contents

[edit] 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.

[edit] Instructors

[edit] Syllabus

  • 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.
  • 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 4: Gene Expression Analysis: Resampling, manipulating trees, gene function enrichment, pathways, FDR, combine comparisons
  • 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.
  • Session 6: SNP Array Analysis: LOH and copy number analysis with sample data; export.
  • Session 7: SNP Array Analysis: Intricacies of copy number and LOH analysis, parameters used
  • Session 8: SNP Array Analysis: Allele sharing analysis, linkage analysis; automation in dChip

[edit] 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.)

[edit] Registration

Registration for courses at Bioinformatics.Org takes two steps:

Step 1
If you haven't already done so, create an online 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 online 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

[edit] Tuition & discounts

Payee and costs:

  • Employer (for-profit & government): $1200 USD
  • Employer (non-profit & academic): $800 USD
  • Yourself (not being reimbursed): $400 USD

Additional discounts are available as follows:

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

[edit] Logistics

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 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 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.

[edit] 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.

[edit] Additional information

Please contact us for questions or additional information.

[edit] See also

Retrieved from "http://www.bioinformatics.org/wiki/BI201C_dChip_for_Gene_Expression_and_SNP_Microarray_Data_Analysis"
Personal tools