How Do I Become A BimCore Subscriber?

Please fill out this form or contact Kim Gernert.

What software is available to BIMCORE subscribers and where do I use it?

Currently, BIMCORE has three software packages available to analyze microarrays. They include GeneSpring, Spotfire, and Affymetrix. GeneSpring can be downloaded onto a local computer but can only have 2 concurrent users at a time on the Emory Server. Spotfire (DecisionSite, Functional Genomics, and Statistics) can only be accessed onsite at BIMCORE's lab (G236 Biochemistry Connector) on the two workstaions. The Affymetrix Microarray Suite can only be used onsite at BimCore's lab (G236 Biochemistry Connector) on one workstation. See map for details.

How do I request additional software?

Contact Kim M. Gernert.

What do I do if I have other questions that are not answered here?

For Affymetrix software, you should go to the Help section on the Affymetrix website. For GeneSpring, go to their Frequently Asked Questions. For Spotfire questions, they have an e-support team where you can ask questions and one of their technical support people will answer your questions. Spotfire also has a Knowledge Base, which describes common errors seen in Spotfire and some frequently asked questions.

What other software is available on this workstation?

Cluster and Tree View from Dr. Eisen's Lab are currently installed and available.-->

How do I use the DNA Core Affymetrix Gene Chip Station?

Each person is required to be an authorized user on the Affymetrix machine prior to using it. In order to become an authorized user, you need to go through training. Once you are an authorized user, you will receive access to the scheduling calender and a user ID and password for the machine. Billing for the use of the machine is charged to the calendered user. There are two training options at this time.

1. Kim Woller from Affymetrix can train for $1250/ day for 1 or 2 days training.
2. Byron Ford at the CBN Affymetrix facility can train.

Please contact Kim Gernert for further details.

Who can I contact for technical support?

Affymetrix Technical support line: 1-888-DNA-CHIP. Emory's Affymetrix personnel Kimberly Woller, 1-888-DNA-CHIP x 4103, kimberly_woller@affymetrix.com .

Is There A Quick Guide For Affymetrix?

Yes, we have prepared a Quick Guide. You can also consult Affymetrix's Expression Analysis Technical Manual for assistance.

What Is The Affymetrix Microarray Suite?

The Affymetrix Microarray Suite uses application-specific high-density GeneChip oligonucleotide probe arrays to efficiently acquire and analyze genetic information for gene expression, genotyping, and nucleotide variant detection. The Microarray Suite Algorithms determine absolute or comparison gene expression results, perform nucleotide variant detection, or identify genotype, depending on the type of probe array assay.

What is the Affymetrix Micro DB software?

Processes data for use with Data Mining Tool and for translation to GATC format for use with outside software.

What is the Affymetrix Data Mining Tool software?

Data Mining Tool (DMT) version 3.0 contains a variety of powerful features for filtering and sorting expression results, enabling you to rapidly identify your most significant results. The software provides the tools you need to perform complex analyses on your data for a more comprehensive interpretation of your results, including clustering methods (Self-Organizing Maps and a modified Pearson's Correlation Coefficient method).

See the available DataMining Tool Tutorial. Includes the following topics:

     Caluclate summary statistics of replicates
     Summarize qualitative data
     Evaluate differences between 2 tissues
     Use comparison ranking to evaluate difference call consistency
     Perform cluster analysis using self-organizing maps algorithm

Once I obtain a list of Probe IDs that I am interested in, how do I find out more information about the genes that the probes are targeted for?

Use the NetAffx Analysis Center on the Affymetrix website. There you can submit a text list of probe ids (up to 500), in the Batch query to the analysis center and it can give you information on the Gene Ids, Accession number, and functional annotations for the genes related to the probe sets submitted.

Is it possible to transfer my databases from DMT 2.0 to 3.0?

If you have an older (DMT 2.0) dataset that you want to transfer to the new DMT 3.0 , you must first use MicroDB to Archive that database. When the switch is made to DMT 3.0, you can use the "Restore Archive" feature of MicroDB to import your old dataset and it will be available as a registerd database in the DMT.

Databases which have not been archived cannot be read under 5.0. However one can use the MAS 5.0 to re-read the CHP file and recreate the database. Unfortunately there is no way to directly read the older databases.

Should I Worry About Data Integrity When Using Different Version of the Software?

For detailed information about the differences between versions 3.3 and 4.0.1 of Affymetrix's suite and their implication for your data's integrity and compatibility, please see our versions summary.

How do I import my data from Affymetrix into Spotfire?

There are two ways to get data into Spotfire, you can copy and paste directly from an EXCEL spreadsheet or use Spotfire's import wizard. Note that if you are doing comparisons and want the change calls that Affymetrix software can give you, you need to perform your comparisons in Microarray Suite first, and save this data to your Affymetrix file before importing into Spotfire.

How do I import data from Affymetrix into GeneSpring?

You have to save your data as a text delimited file to import it into GeneSpring for datamining. GeneSpring will not allow you to directly import files from other software.