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  • BI202 SNP Genotyping

    This course helps to demystify Affymetrix analysis so that any researcher can take the basic steps to go from a chip image to genotypes, for each SNP, and to the copy number or linkage associated with the SNPs in given samples. Various tools will be covered, such as GCOS, GTYPE, BRLMM, CNAT, Excel, MATLAB, and free tools like dChip. It is geared towards researchers who conduct microarray-based SNP genotyping experiments to study genome-wide polymorphisms and then use the information for genotyping and linkage analysis. Most scientists are not able to analyze resulting microarray data themselves and are not able to get desired results using traditional tools like Microsoft Word and Excel, or the advanced software provided by commercial vendors. The free 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.

    Sessions 1 & 2
    Introduction to GCOS -- the environment, creating and saving experiments, importing and exporting data, normalization settings, from DAT->CEL->CHP files and their significance, importing and exporting data, SNP chip layout and algorithms for generating genotypes
    Sessions 3 & 4
    GTYPE, BRLMM for generating genotypes, sample mismatch report, gender calls, pedigree check, creating virtual sets, and copy number analysis
    Sessions 5 & 6
    dChip software: importing SNP data and annotation information into dChip, LOH analysis, copy number analysis, linkage disequilibrium analysis, allele sharing analysis, and exporting to Excel
    Sessions 7 & 8
    MATLAB: importing SNP data in MATLAB, manipulating and filtering SNP genotypes, automating tasks using API to Affymetrix SDK, building custom user interfaces for advanced applications, and exporting to Excel

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


    Registration for courses at 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.


    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).


    This course is certified by, 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 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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