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Table of Contents
Introduction to ChipInspector.............................................................................................................. 4
What is Genomatix ChipInspector?................................................................................................... 4
Data Analysis................................................................................................................................... 4
Analysis Background .................................................................................................................... 4
File Requirements ........................................................................................................................ 6
Steps in the Statistical Analysis of Microarrays in ChipInspector..................................................... 6
Technical Requirements ...................................................................................................................... 9
Memory Requirements..................................................................................................................... 9
Operating Systems .......................................................................................................................... 9
Java Runtime Environment ............................................................................................................ 10
Browser......................................................................................................................................... 11
Installation and Configuration of ChipInspector.................................................................................. 12
Download...................................................................................................................................... 12
Get Login and Password ................................................................................................................ 14
Registration ............................................................................................................................... 14
Change Password....................................................................................................................... 16
Password Policy ......................................................................................................................... 17
Installation .................................................................................................................................... 18
Configuration of ChipInspector....................................................................................................... 20
Proxy Configuration.................................................................................................................... 21
SSL Configuration....................................................................................................................... 22
Check for Updates...................................................................................................................... 23
Configuration of Statistical Analysis Behavior .............................................................................. 26
Data Storage Settings ................................................................................................................ 27
The ChipInspector Workspace Area ................................................................................................... 28
Project Management Panel ............................................................................................................ 28
Main Panel .................................................................................................................................... 28
Memory Monitor ............................................................................................................................ 29
Log File Monitor............................................................................................................................. 29
Project Tree...................................................................................................................................... 30
Creating a New Project Tree .......................................................................................................... 30
Opening an Existing Project Tree ................................................................................................... 30
Saving the Project Tree ................................................................................................................. 30
Deleting a Project Tree .................................................................................................................. 30
Projects ............................................................................................................................................ 31
Creating a New Project .................................................................................................................. 31
Importing Data Files into a Project ................................................................................................. 32
Data Import Interface ................................................................................................................ 33
Editing a Project ............................................................................................................................ 37
Deleting a Project .......................................................................................................................... 37
Project Data Files .......................................................................................................................... 37
Editing a Data File...................................................................................................................... 37
Deleting a Data File.................................................................................................................... 38
Analyses ........................................................................................................................................... 38
Creating a New Analysis ................................................................................................................ 38
Editing an Analysis......................................................................................................................... 39
Designing an Analysis .................................................................................................................... 39
Analysis Settings ........................................................................................................................ 42
Starting an Analysis.................................................................................................................... 46
Committing an Analysis for a Batch Job ...................................................................................... 47
Creating and Starting a Batch Job............................................................................................... 47
Redoing an Analysis....................................................................................................................... 49
Statistics Curve ................................................................................................................................. 49
Cluster View...................................................................................................................................... 52
Result List......................................................................................................................................... 53
Exporting Results........................................................................................................................... 54
© 2007 Genomatix Software GmbH
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