Download User`s Manual - J

J-Express Pro User’s Manual
3.27 DATASET REPOSITORY ....................................................................................145
3.27.1 Starting the repository browser and registering an account .............146
3.27.2 Server settings and logging in............................................................147
3.27.3 Viewing and editing datasets and folders ..........................................147
3.27.4 Saving new datasets to a repository...................................................147
3.27.5 Trouble shooting: Network settings and firewalls .............................148
3.27.6 Setting up a dedicated server.............................................................148
3.28 PLUGINS ..........................................................................................................148
3.28.1 Creating Plugins ................................................................................148
4
J-Express Pro User’s Manual
1
Introduction
METHOD AND ALGORITHM DESCRIPTION ........................................150
4.1 DISTANCE MEASURES ........................................................................................150
4.1.1
Similarity search ................................................................................153
4.2 CLUSTERING......................................................................................................153
4.2.1
K-means clustering ............................................................................154
4.2.2
Hierarchical clustering......................................................................155
4.3 PROJECTION METHODS ......................................................................................160
4.3.1
Principal Component Analysis (PCA) ...............................................160
4.4 SELF-ORGANIZING MAPS ...................................................................................163
4.4.1
Principle.............................................................................................163
4.4.2
The neighborhood kernel ...................................................................164
4.4.3
The Elastic surface.............................................................................166
4.4.4
An example of the SOM algorithm.....................................................167
5
REGULAR EXPRESSIONS...........................................................................169
5.1.1
Regular-expression constructs...........................................................169
J-Express Pro in use.
The J-Express Pro package allows the user to load a data set resulting from a set of
microarray experiments and to apply a number of analysis methods, view the results, and
produce publication quality figures. The analysis methods include clustering methods
(hierarchical and K-means clustering), projection methods (Principal Component
Analysis), correspondence analysis, and self-organizing maps. J-Express Pro also provides
feature selection methods to identify genes differentiating between classes of arrays. A
scripting interface is also available, allowing streamlining and automatically repeating
standard analyses. J-Express supports import of MAGE-ML data, facilitating exchange of
data with microarray databases including ArrayExpress and BASE. J-Express Pro has an
integral project management functionality that helps the user keep track of the datasets,
analyses performed, etc. A Server/client system built into J-express allows multiple users
to work on a single project simultaneously.
6