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GeneChip® Command Console (AGCC)
FREQUENTLY ASKED QUESTIONS
What is Affymetrix GeneChip® Command Console® (AGCC) software?
When will Command Console software be launched?
What modules are included with Command Console?
What are the key benefits of Command Console software?
How will Command Console software improve data management?
How will Command Console software improve the ability to share data with collaborators and end users?
Which arrays are supported by Command Console software?
Which instruments are supported by Command Console software?
Which software supports the Fluidics Station 400 and Agilent Technologies' GeneArray® 2500 Scanner?
What is the webserver in Command Console used for?
Is the Command Console web server hosted by customers or by Affymetrix?
Should customers be concerned with security when using the Web Server in their environment?
Will GCOS still be available?
Will GCOS still be supported?
How does Command Console differ from GCOS in terms of workflow?
Are the data formats different between GCOS and Command Console?
Why are different data formats for GCOS and Command Console necessary?
How are the new Command Console file formats better than those for GCOS?
How is data converted from GCOS format to Command Console format and vice versa?
Do users need to convert all GCOS data to the Command Console format?
Can data exist as a mixture of GCOS and Command Console formats?
Which GCOS features are not supported in Command Console?
Are the Affymetrix Analysis Data Model (AADM) and Data Mining Tool (DMT) supported by Command Console?
What happens to GCOS if Command Console is installed on the same workstation?
Must GCOS be uninstalled in order to install Command Console?
Will the data be identical when generated from Command Console software versus GCOS?
Where can customers learn more about Command Console?

COMMAND CONSOLE WORKFLOW

What are data roots?
What are projects?
What are sample attributes and sample attribute files?
What are templates?
How is data security and backup implemented in Command Console?
How are library files imported into Command Console?
How is the Library File Importer installed?
What are the library files for Command Console?
Where can users learn more about the workflow or specific steps or features in the software?
What is sample/array registration?
Can arrays be registered in batches?
Which files are required to use a fluidics station?
Which files are required to scan an array?
How are DAT and CEL data files analyzed?
Can DAT image files be viewed while the array scan is in progress?
How are DAT files gridded and/or re-grided manually?
When is array registration necessary?
What are the benefits of array registration?
How are arrays processed when the fluidics station and scanner are controlled by different workstations?
How are CHP files created from Command Console CEL files?
Can report files similar to those produced in GCOS be generated by the Command Console platform?
How is Command Console CEL data published to a GCOS Publish database?

DATA MANAGEMENT

How do users find their data in Command Console?
Do users have to copy the sample/array attribute file with CEL data to other systems?
Can users open, view or analyze GCOS data in Command Console?

INSTALLATION

Do users have to install the Command Console software on computers that will run downstream analysis on Command Console data?
How do users download and install Command Console software?
How do users install Command Console on data analysis computers (non-instrument control workstations)?
Which operating systems and web browsers have been tested with Command Console?
What are the two versions of Command Console?
What is the Command Console Standalone?
What is the Command Console Workgroup?
What are the hardware and software requirements for Command Console?
Are there any software packages that are not compatible with Command Console?
Can Command Console coexist with GCOS on the same workstation?
Are there separate installers for Command Console Standalone and Workgroup?
How is the Command Console installer packaged?