Download J-Express Pro User Manual

J-Express Pro User’s Manual
Table of contents
1 INTRODUCTION.....................................................................................................6
2 GETTING STARTED..............................................................................................7
2.1 DOWNLOADING AND INSTALLING J-EXPRESS PRO ...........................................................7
2.1.1 System requirements.....................................................................................7
2.1.2 Download and setup......................................................................................7
2.2 INTRODUCTION TO J-EXPRESS PRO..............................................................................9
2.2.1 Loading Gene Expression Data..................................................................10
2.2.2 The Project Tree
..............................................................................................................................13
2.2.3 Hierarchical Clustering..............................................................................13
2.2.4 K-Means Clustering....................................................................................14
2.2.5 Principal component analysis (PCA)..........................................................15
2.2.6 Self Organizing Map (SOM).......................................................................18
2.2.7 Gene Graph viewer.....................................................................................19
2.2.8 Search and sort...........................................................................................19
2.2.9 Finding Similar Profiles..............................................................................20
2.2.10 Customizing the External database links.................................................21
2.2.11 Creating and managing groups...............................................................22
2.2.12 Managing Projects....................................................................................23
3 REFERENCE - THE COMPLETE J-EXPRESS PRO GUIDE........................25
3.1 PROJECTS...............................................................................................................25
3.1.1 The J-Express Pro tables............................................................................25
New projects .......................................................................................................25
3.1.2 Importing gene expression data manually into J-Express Pro...................26
3.1.3 Importing Illumina data..............................................................................29
3.1.4 Importing Spot Intensity (Raw) Data..........................................................34
3.1.5 Refining / Processing Raw Data.................................................................37
3.1.6 GenePix.......................................................................................................44
3.1.7 Affymetrix....................................................................................................50
3.1.8 Tabular........................................................................................................51
3.1.9 Project Dataset...........................................................................................54
3.2 ROBUST MULTI-ARRAY AVERAGE (RMA) ...............................................................56
3.2.1 Memory usage:............................................................................................56
3.2.2 How to load affymetrix data using RMA:...................................................57
3.3 THE PROJECT WORKSPACE.......................................................................................58
3.3.1 Project Thumbnails and Info/Metadata......................................................61
3.3.2 Showing / hiding project workspace windows............................................64
3.3.3 Changing colors and fonts .........................................................................64
3.3.4 Saving Projects and Exporting data...........................................................67
3.3.5 Creating and Managing Groups.................................................................67
3.3.6 Defining sample pairs.................................................................................69
3.3.7 Managing Groups:......................................................................................71
3.4 THE GENE GRAPH VIEWER......................................................................................73