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[NEU MS in Bioinformatics]
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  • BI203 dChip for Gene Expression and SNP Microarray Data Analysis

    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.

    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

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

    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 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

     

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