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Product FAQ

What are the GeneChip Operating Software (GCOS) and GCOS Server Software (GCOS Server) products?

Answer

The GeneChip Operating Software (GCOS) is an operating system software that controls our instruments, acquires data, and executes gene expression analysis. In addition, GCOS contains an embedded database that manages both experiment information and data. Stratagene Array Assist Lite, Affymetrix GeneChip Sequence Analysis Software (GSEQ), Affymetrix GeneChip Genotyping Analysis Software (GTYPE), Affymetrix GeneChip Targeted Genotyping Analysis Software (GTGS) use data from the GCOS Database for gene expression cluster/statistical analysis, sequencing analysis and genotyping data analysis, respectively.

GCOS desktop version (client) can be conveniently upgraded to GCOS Server. With GCOS Server, customers benefit from increased systems flexibility, streamlined user interface integration, enhanced automation, and robust data handling and security. Using either an Oracle or SQL based server, researchers can perform a variety of data management tasks and data queries. Plus, extensive security features are available to allow users secure access to their data.

Answer Id: E13556

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Product FAQ

What quality metrics can I examine to determine if dim or bright hybridizations have impacted my data?

Answer

Use either All_mean or PM mean to assay for hybridization intensity. All_mean is a probe-set metric. PM_mean is a probe-level metric, and is the mean of perfect match raw intensities prior to any transformations, such as normalization or probe summarization. PM_mean and All_mean can be compared to understand the effect that data processing steps have on the average intensity of an array because All_mean has been subject to any data transformations that have been performed during signal estimation and normalization. Apparent outliers only based on PM_mean can be ignored when corrected through data normalization in All_mean.

Answer Id: E14026

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Product FAQ

Do I need to apply the high-resolution scanning patch for the HG-U133 2.0 Arrays?

Answer

Below is a list of circumstances and clarification regarding whether or not the high resolution scanning patch needs to be applied. Keep in mind that the high resolution scanning patch must only be applied on top of GCOS, not AGCC.

a. GeneChip Scanner 3000 (serial numbers 502xxxxx): The instrument service engineer has applied the high-resolution scanning patch to the computer that is controlling the GeneChip Scanner 3000 at installation, but not to the workstations or servers (see c and d below).

b. GeneChip Scanner 3000 (serial numbers 501xxxxx): The instrument service engineer will apply the high-resolution scanning patch to the computer that is controlling the GeneChip Scanner 3000 at the time of the upgrade, but not to the workstations or servers (see c and d below).

c. Analysis workstations and clients: You must apply the high-resolution scanning patch to GCOS analysis workstations.

d. GCOS Server upgrade: Your GCOS database administrator or an Affymetrix Software Support Engineer needs to apply the high-resolution scanning patch in coordination with the upgrade of server to GCOS.

e. Installation of library files post scanner installation or upgrade: The high-resolution scanning patch must be reapplied following the installation of library files for arrays that precede the HG-U133A 2.0 and HG-U133 Plus 2.0 Arrays. The HG-U133A 2.0 and HG-U133 Plus 2.0 library files are high-resolution-scanning ready. The error message "cannot read the parameters for probe array type from the database" appears when one tries to scan an array on a GeneChip Scanner 3000 high-resolution scanner when the high-resolution scanning patch has not been applied.

Answer Id: E13778

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Product FAQ

Why is the bgrd_mean (background) value sometimes higher than that of PM_mean (signal)?

Answer

The mean of the background probe signal values is based on background probes defined in the background probe file, which are by default the anti-genomic probes. Anti-genomic probes consist of about 1,000 probes for each level of GC content (0 to 25) with no homology to most studied organisms. This set has a higher GC content than the average probe on the array, and therefore can have relatively higher signal values than the mean of all probes (PM_mean).

Answer Id: E14027

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Product FAQ

What are the minimum and recommended hardware requirements for GTC 4.2?

Answer

Minimum hardware requirements:
-Memory (RAM): 16 GB
-Hard drive: 150 GB*
-Processor: 2.0 GHz Intel Pentium or higher

Recommended hardware requirements:
-Memory (RAM): 4 GB
-Hard drive: 100 GB*
-Processor: 2.5 GHz Intel Quad Core or higher

*Note: The hard drive requirements are for GTC 3.0.1 only; data needs additional space.

Answer Id: E13669

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Product FAQ

What are the instrumentation and software requirements for Mouse 430 2.0 Arrays?

Answer

For array hybridization, washing, staining and scanning, the following instrumentation is required:

-GeneChip Scanner 3000 7G
-Fluidics Station 450
-Hybridization Oven 640 or Hybridization Oven 645

Data acquisition and analysis of Mouse 430 2.0 Arrays requires the following software:

-GeneChip: Command Console Software
-Expression Console Software

Answer Id: E13708

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Product FAQ

Where can I obtain the high-resolution scanning patch for the HG-U133 2.0 Arrays?

Answer

Please contact Technical Support to obtain the high-resolution scanning patch.

Answer Id: E13779

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Product FAQ

For GeneChip experiments, can I measure the quality of a single hybridization without the rest of the experiment?

Answer

We does not recommend measuring the quality of a single-array performance without consideration for the rest of the experiment. In large-scale expression experiments using similar sample types, researchers are likely to develop their own single-array guidelines on what metric values are predictive of high- or poor-quality samples. However, these guidelines are likely to be dependent on sample type, and we are unable to recommend such guidelines for all possible situations. Note that the trend toward favoring model-based signal estimation algorithms (for all microarray experiments even beyond the Affymetrix platform) makes single-array quality determination very difficult due to the necessity of simultaneously analyzing multiple arrays to calculate signal estimates.

Answer Id: E14028

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Product FAQ

How do I know if my GeneChip Scanner 3000 has been enabled for high-resolution scanning that is needed for the Mouse 430 2.0 Arrays?

Answer

a. GeneChip Scanner 3000s that were shipped after September 15, 2003 with serial number 502xxxxx are enabled for high-resolution scanning.

b. GeneChip Scanner 3000s that were shipped prior to September 15, 2003 with serial number 501xxxxx that have had the GeneChip Scanner 3000 High-Resolution Update installed by an instrument service engineer are enabled for high-resolution scanning. A sticker is applied to the rear of the scanner to indicate that the upgrade has been performed

c. Contact 888-DNA-CHIP or your local Affymetrix technical support to inquire about a scanner upgrade.

Answer Id: E13709

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Product FAQ

How much memory is needed to store the data from a single HG-U133 Plus 2.0 Array?

Answer

About 175 MB.

Answer Id: E13780

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Product FAQ

What is the NetAffx Analysis Center?

Answer

The NetAffx Analysis Center is the most comprehensive resource of integrated array contents and functional annotations available. The flexible query capabilities provided help you retrieve biological information for specific probe sets. Please read our Analysis Center tutorial for more information (http://www.affymetrix.com/analysis/index.affx#1_1).

Answer Id: E13455

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Product FAQ

Are there any service providers for the Axiom Genome-Wide BOS 1 Array Plate?

Answer

A number of service providers have experience running the Axiom Assay and the genotyping call algorithm that is used with the Axiom Genome-Wide BOS 1 Array Plate.

Answer Id: E14046

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Product FAQ

What are the library files for Command Console Software?

Answer

Media file - contains information about the media type on which the array is printed, such as a cartridge or 96-well plate.
Master file - contains array-specific design information and replaces the cif file. It also identifies the analysis library file packages and scan parameter files.
Workflow file - lists the actions to be performed on each probe array type, such as gridding and CEL file generation. The file also includes references to the appropriate algorithm parameter file.
Algorithm parameter file - contains the parameters for an algorithm.

Answer Id: E14241

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Product FAQ

Is it necessary to uninstall prior versions before installing GTC 4.2?

Answer

Genotyping Console 4.2 will upgrade from previous versions 4.1, 4.1.1, 4.1.2, 4.1.3 and 4.1.4. The GTC 4.2 installer will remove the previous version as well as install the latest version. If Matlab is installed, the installer will ask you if you would like to remove it. Testing has not been performed to upgrade from GTC 1.0, 2.x, 3.x.

Answer Id: E13670

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Product FAQ

Which kit do I need to purchase to run the PluriTest Assay?

Answer

Customers should purchase the GeneChip PrimeView Global Gene Expression Profile Assay (Cat. No. 905406 or 905407).

 

Answer Id: E16776

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