Transcript B-Introduction-Handout - Hennig

Bioinformatics for
“Gene Expression Analysis
in Diagnostic Medicine”
Follow-up Course, 20 to 25 November 2006
CAS-MPG Partner Institute for
Computation Biology, Shanghai
1
Handout - Monday morning:
1. Goals of this Course
2. Course Outline
3. TIGR Software Suite TM4
4. Using Apple computers
(and viewing MA slides)
2
Goals
1. Obtain raw expression values from
scanned slides
2. Perform quality checks
3. Produce comparable expression values
through normalization
4. Explore data with clustering methods
5. Find significantly expressed genes
3
Outline
|
Monday
Tuesday
Wednesday
Thursday
Friday
--------------------+-----------------------------------------------------------------------------------------------8:30
Computer| Seminar room:
Practise with
Practise with
Practise with
Practise with
room
| - Welcome
Manila data:
Manila data:
MeV on:
drosophila data:
| - Introduction
- Get raw values
- Get expression
- Differential
- Clustering
10:30
(Coffee)
| Computer room:
(Spotfinder)
data (MIDAS)
expression
(Mev)
| - using Macs
- Clustering (MeV) - Multiple
- Compare to
| - starting
testing
Angela's work
|
Spotfinder
--------------------+-----------------------------------------------------------------------------------------------13:30
Lunch
|
--------------------+-----------------------------------------------------------------------------------------------14:30
Seminar| Lectures:
Lectures:
Lectures
Lectures
Final:
room
| - Image processing
- Normalisation
(Christ.+Dennis): (Angela):
- Demo of
|
(Spotfinder)
(MIDAS software) - Differential
- Identification
databases
16:00
(Coffee)
| - Quality checks
- Clustering
Expresssion
of glial gene
- General
| - Workflow and
methods
- Multiple
in drosophila
discussion
|
data file types
(MeV software)
Testing
- Discussion of
|
experiment design
--------------------|-----------------------------------------------------------------------------------------------17:30
End
|
4
TIGR Software Suite TM5
Printer
Scanner
.tiff Image File
Image
Analysis
Raw Gene Expression
Data
Gene Annotation
Normalization /
Filtering
Normalized Data with
Gene Annotation
Expression
Analysis
Interpretation of
Analysis Results
5
Using Apple computers
The Menu bar of the current application
Two Finder windows
(like Windows Explorer)
The
Finder
Sidebar
provides
links to
important
folders
The Dock holds running and most used applications
6
Using Apple computers
The Apple menu
holds general
items, such as:
Logout
Here is all our course data:
/picb/course/
Preferences
Finder
Safari Webbrowser
Activity Monitor
7
Using Apple computers
Practising steps:
1. Obtain login account and password from lecturer
2. Login and familiarize with Finder
3. Locate /Applications/System Preferences.app and use it to enable right
mouse button
4. Remove unneeded items from Finder Sidebar and from Dock
5. Locate /Applications/Utilities/Activity Monitor.app and activate Memory
Usage and CPU Monitor
6. Locate /picb/course/Applications and add it to Finder Sidebar
7. Start TIGR-Spotfinder311.app (through Sidebar)
8. In Spotfinder, view some Microarray slides from Manila, located in
/picb/course/10-Manila-Slides/
8