# CS102B R for Biologists, Level 2

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 Revision as of 01:02, 18 December 2007 (view source)Cody (Talk | contribs) (→Course schedule)← Older edit Latest revision as of 12:51, 24 September 2012 (view source)Admin (Talk | contribs) m (→Syllabus) (23 intermediate revisions not shown) Line 1: Line 1: - ==Objective== + ==Objectives== Taught in the context of biological research, this course helps biologists understand the data analysis and visualization language R. It is a continuation of [[CS101B R for Biologists, Level 1]] and covers advanced topics and projects. Taught in the context of biological research, this course helps biologists understand the data analysis and visualization language R. It is a continuation of [[CS101B R for Biologists, Level 1]] and covers advanced topics and projects. - ==Course outline== + ==Syllabus== - * Day 1: Basic R commands for loading, manipulating and visualizing data + * Session 1: Review of basic R commands for loading, manipulating and visualizing data ** How to create, manage and visualize data in R objects – vectors, matrices, data frames, lists ** How to create, manage and visualize data in R objects – vectors, matrices, data frames, lists ** Good programming practices ** Good programming practices ** Specials notes, shortcuts, and basic commands that you may have forgotten ** Specials notes, shortcuts, and basic commands that you may have forgotten ** Project: create a function that will compute the t-statistic, fold change, difference and p-value for all genes, and filter the data to keep the up- or down-regulated genes. ** Project: create a function that will compute the t-statistic, fold change, difference and p-value for all genes, and filter the data to keep the up- or down-regulated genes. - * Day 2: Case studies in linear regression, t-test, anova + * Session 2: Case studies in linear regression, t-test, anova - * Day 3: Advanced graphics with par() + * Session 3: Advanced graphics with par() - * Day 4: Bioconductor objects and algorithms, and getting differentially regulated genes from Affymetrix CEL files + * Session 4: Bioconductor objects and algorithms, and getting differentially regulated genes from Affymetrix CEL files ** More case studies ** More case studies - * Day 5: Project: use limmaGUI or affylmGUI datasets to perform an analysis. + * Session 5: Project: use limmaGUI or affylmGUI datasets to perform an analysis. - ==Course schedule== + {{Course footer - + |hours=3 - This course has been offered several times. Access to completed courses is available to enrolled students only, because of privacy and confidentiality issues. If you are interested in an upcoming course, register using instructions below. + }} - + - * [http://edu.bioinformatics.org/ATG Course ATG (online), January 28-February 2, 2008] + - * [http://edu.bioinformatics.org/ACT Course ACT (online), December 3-7, 2007] + - * [http://edu.bioinformatics.org/TT/site Course TT (online), September 24-28, 2007] + - * [http://edu.bioinformatics.org/GC/site Course GC (online), July 9-13, 2007] + - * [http://edu.bioinformatics.org/AS/site Course AS (online), April 9-13, 2007] + - * [http://edu.bioinformatics.org/AH/site Course AH (online), February 19-23, 2007] + - * [http://edu.bioinformatics.org/AD/site Course AD (online), January 15-19, 2007] + - + - ==Registration== + - + - 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. + - + - For an additional USD \$49, students who attend this course may order data discs containing full-resolution lecture videos and extra copies of the slides, scripts and data files. + - + - Registration deadline: When full + - + - ===[[Tuition discounts]]=== + - + - * Returning student discount: A 20% (rounded up) discount applies for students who have paid the base tuition (without a similar discount) for a course at Bioinformatics.Org that does '''''not''''' fall in the CS101 range (e.g., CS102A/B) (please use the mail-in registration form rather than PayPal if taking this discount). + - * Cluster course discount: A 50% (rounded up) discount (cannot be combined with the 20% discount) applies for students who have paid the base tuition for a course that '''''does''''' fall in the CS101 range (please use the mail-in registration form rather than PayPal if taking this discount). + - + - Tuition (all prices USD): + - + -
Base tuitionIf taken with a non-CS101
course at base tuition
If taken with another CS101
course at base tuition
Commercial\$595\$476\$298
Non-profit/academic\$397\$318\$199
+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - For full-time students and the unemployed, please inquire about an additional discount (verification required). + - + - ==Logistics== + - + - http://edu.bioinformatics.org/images/asap_logo.png + - + - Online courses are offered on the ASAP online meeting system.  Access information will be provided prior to the start of the course. Each lecture will last 45 to 90 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. + - + - 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].  Please [[ASAP requirements|check the specific system requirements for your computer]].  A microphone and webcam is not required for this course.  The necessary software, lecture notes and exercises will be provided. + - + -
+ - ''ASAP is a trademark of Convoq, Inc.
Other names are trademarks of their respective owners.'' + -
+ - + - ==Additional information== + - + - 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 +1 508 890 8600. + - + - ==See also== + - + - * [[Educational services|Educational services at Bioinformatics.Org]] +

## Objectives

Taught in the context of biological research, this course helps biologists understand the data analysis and visualization language R. It is a continuation of CS101B R for Biologists, Level 1 and covers advanced topics and projects.

## Syllabus

• Session 1: Review of basic R commands for loading, manipulating and visualizing data
• How to create, manage and visualize data in R objects – vectors, matrices, data frames, lists
• Good programming practices
• Specials notes, shortcuts, and basic commands that you may have forgotten
• Project: create a function that will compute the t-statistic, fold change, difference and p-value for all genes, and filter the data to keep the up- or down-regulated genes.
• Session 2: Case studies in linear regression, t-test, anova
• Session 3: Advanced graphics with par()
• Session 4: Bioconductor objects and algorithms, and getting differentially regulated genes from Affymetrix CEL files
• More case studies
• Session 5: Project: use limmaGUI or affylmGUI datasets to perform an analysis.

## 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
• For-profit & government: \$500 USD
• Non-profit & self-pay: \$300 USD
Live instruction held on-site
• For-profit & government: \$600 USD
• Non-profit & self-pay: \$400 USD
On-demand instruction held on-line
• For-profit & government: \$300 USD
• Non-profit & self-pay: \$200 USD

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).

## 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 an hour, 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 3 "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.