CS102B R for Biologists, Level 2

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==Course outline==
==Course outline==
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Day 1
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* Day 1: Basic R commands for loading, manipulating and visualizing data
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* Basic R commands for loading, manipulating and visualizing data
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** 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
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** 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.
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* Day 2: Case studies in linear regression, t-test, anova
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* Day 3: Advanced graphics with par()
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* Day 4: Bioconductor objects and algorithms, and getting differentially regulated genes from Affymetrix CEL files
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** More case studies
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* Day 5: Project: use limmaGUI or affylmGUI datasets to perform an analysis.
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Day 2
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==Course schedule==
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* 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.
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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.
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* Case studies in linear regression, t-test, anova
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* [http://edu.bioinformatics.org/TT/site Course TT, September 24-28, 2007, 17:00-18:30 UTC (Registration Open)]
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* [http://edu.bioinformatics.org/GC/site Course GC (online), July 9-13, 2007]
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* [http://edu.bioinformatics.org/AS/site Course AS (online), April 9-13, 2007]
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* [http://edu.bioinformatics.org/AH/site Course AH (online), February 19-23, 2007]
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* [http://edu.bioinformatics.org/AD/site Course AD (online), January 15-19, 2007]
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Day 3
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==Registration==
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* Advanced graphics with par()
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Day 4
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* Bioconductor objects and algorithms, and getting differentially regulated genes from Affymetrix CEL files
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* More case studies
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DAY 5
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* Project: use limmaGUI or affylmGUI datasets to perform an analysis.
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==Logistics==
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http://edu.bioinformatics.org/images/asap_logo.png
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Locale: This course is offered on the ASAP online meeting system.  Access information will be provided prior to the start of the course.
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Dates & times: Please see the course schedule below for the next time that this course will run. 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.
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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.
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.
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Technical Requirements: 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.
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Registration deadline: When full
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==Prerequisites (entry conditions)==
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Students should have taken [[CS101B R for Biologists, Level 1]] or have equivalent experience.
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==Certification==
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This course is certified by the [[Bioinformatics Organization|Bioinformatics Organization, Inc.]], the largest international affiliation in the field, and it will count as '''8''' "Continuing Scientific Education" (CSE) credits (one credit per contact hour) within the Organization. Students completing the course will receive a certificate attesting to that.
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==Course schedule==
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* [http://edu.bioinformatics.org/TT/site Course TT, September 24-28, 2007, 17:00-18:30 UTC]
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==Registration==
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===[[Tuition discounts]]===
===[[Tuition discounts]]===
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For full-time students and the unemployed, please inquire about an additional discount (verification required).
For full-time students and the unemployed, please inquire about an additional discount (verification required).
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Registration deadline: When full
 
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Please [https://edu.bioinformatics.org/login/signup.php create an account] before registering, if you haven't already done so.  The educational website at Bioinformatics.Org requires a separate username and password.
 
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Available payment methods:
 
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# Online registration form (account required; please use the link in the course schedule above)<br />''Use this form only for credit card payments (via secured PayPal)''.
 
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# [http://edu.bioinformatics.org/download/registration_form.pdf Mail-in registration form] (~150 kB PDF)<br />''Use this form if paying by check (US bank accounts only), credit card or corporate purchase order''.
 
==Additional information==
==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.
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.
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<div style="border-top: solid 1px black; font-size: small; margin: 3em 0em 0em 1em; width: 20em;">
 
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''ASAP is a trademark of Convoq, Inc.<br />Other names are trademarks of their respective owners.''
 
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</div>
 

Revision as of 00:50, 24 August 2007

Contents

Objective

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

Course schedule

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.

Registration

Registration comprises of two steps. First, 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.

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

Tuition (all prices USD):

Base tuition If 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).

Additional information

If you have any questions, please send a message to J.W. Bizzaro (login required) or call +1 508 890 8600.

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