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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 is SNP quality control (SNPQC), and how should it be used?

Answer

SNPQC is a measure of how well genotype alleles are resolved in the microarray data. In other words, it estimates the distributions of homozygous AA, heterozygous AB, and homozygous BB alleles and calculates the distance between them. The better the separation of these distributions, the better the ability to identify a genotype based on its cluster position. A low SNPQC value indicates that the quality of the SNP allele data is compromised due to higher noise within the array, which compromises the overall quality and clarity of results.

Answer Id: E13843

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Product FAQ

Can regions displayed in the heat map viewer be linked to external public databases?

Answer

Yes, regions selected in the heat map viewer can be viewed at the following public sites:
-UCSC
-Ensembl
-Toronto DGV

Answer Id: E13574

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Product FAQ

Expression Console™ Software displays an error when trying to download library files for the first time after installation of the software. What should I do?

Answer

a. Check Operating System of computer and make sure compatible with the Expression Console version installing.
b. Check to make sure the library path for Expression Console is local and not under “My Documents”. In Expression Console™ software, Edit > Set library path
c. Uninstall Expression Console. Download the Expression Console™ package from the website. Unpackage the download. Right mouse click on the setup.exe file and “run as administrator”. Make sure the library path is local.

Answer Id: E14321

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Product FAQ

What is waviness standard deviation (Waviness-SD), and how should it be used?

Answer

Waviness-SD is a global measure of variation of microarray probes that is insensitive to short-range variation and focuses on long-range variation. Based on an empirical testing dataset, we have determined that array data with Waviness-SD >0.12 has either sample or processing batch effects that will reduce the quality of the copy number calls. Elevated Waviness-SD is not always an indication of too much noise. Elevated waviness with good MAPD and SNPQC metrics can occur in samples with many copy number changes. Therefore, it is advised to check the data when observing elevated waviness with good MAPD and SNPQC. The Waviness-SD metric is applicable to constitutional blood and cell line data. The Waviness-SD metric is not intended for alternative sample types such as cancer samples in which the results may vary as a result of the biological complexity. For these sample types, it is recommended to use the ndwavinessSD.

Answer Id: E13844

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Product FAQ

How often is data updated on NetAffx™ Analysis Center?

Answer

NetAffx™ Analysis Center contains both public and Affymetrix-generated data. Unless otherwise noted, public data representations are updated once every quarter (http://www.affymetrix.com/analysis/index.affx#1_1). Because we have considerable control over the proprietary internal data, we will keep you informed as new data and databanks become available.

Answer Id: E13460

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Product FAQ

How much coverage does the Affymetrix™ Mouse Diversity Genoytping Array provide for my gene of interest?

Answer

To determine how a specific gene is covered by the Mouse Diversity Genotyping Array, please visit the NetAffx™ Analysis Center. Query the gene of interest in the genotyping search field and select the Mouse Diversity Array to return the list of SNPs and their annotations to the gene.

Answer Id: E14147

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Product FAQ

Can GeneChip™ expression arrays be reused?

Answer

No, GeneChip™ expression arrays can only be hybridized with sample once, to ensure the highest quality of data.

Answer Id: E13575

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Product FAQ

The ChAS Database could not be contacted. I get an error when launching ChAS. What should I do?

Answer

In Control Panel \ Administrative Tools \ Service Check the chaspostgresql Service status is running. If not attempt to start the service. If it starts, start the ChAS Database Service. If it starts, restart ChAS and see if the error is resolved. If the chaspostgresql service fails to start check the windows application event log. Look for a recent log file with a lock file "postmaster.pid (Ex. PID 2444) entry. Start task manager and from the toolbar select view and select columns; ensure PID is ticked. Locate the PID number found in the event log and right mouse click and select end task. Go back to services and attempt to restart the chaspostgresql service then the ChAS Database Service.

Answer Id: E14322

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Product FAQ

Why are the PLIER/RMA/MAS5 CHP files from Expression Console Software different than those produced by third-party software packages?

Answer

Two reasons explain why the numbers may be different between the two software applications. First, the development environment and compilers were different between the two software applications, resulting in minutely different behavior with floating point values. Secondly, the parameters used to call the algorithm may be different.

Answer Id: E14011

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Product FAQ

Can I label my samples in advance and hybridize arrays later?

Answer

Yes, store at -20 degrees C for up to two weeks.

Answer Id: E14068

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Product FAQ

I have never performed any small sample target labeling before. Do you have any suggestions for incorporating the Two-Cycle cDNA Synthesis Kit into our routine GeneChip™ microarray analysis?

Answer

The basic principles of the Two-Cycle Target Labeling Assay are very similar to the One-Cycle Standard Protocol, and many of the steps involved may look familiar. However, since it does require manipulation of very small amounts of materials in the 1st cycle, even the most experienced GeneChip™ microarray users may not obtain ideal data when using the Two-Cycle protocol the first time. Therefore, it is suggested that users first read the protocol very carefully, including all notes and tips, and then practice initially with diluted samples that you have previously characterized using the One-Cycle Standard Protocol. This way, you will be starting with materials of good quality and you already know what results to anticipate. Follow common laboratory practices that minimize RNase contamination and use caution at each step to prevent sample loss. [This answer refers to a product that has been discontinued.]

Answer Id: E14362

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Product FAQ

What are the array QC metrics for the CytoScan™ arrays?

Answer

CytoScan™ HD and 750K arrays use the following QC metrics:
SNPQC greater than or equal to 15
MAPD less than or equal to 0.25
Waviness-SD less than or equal to 0.12

CytoScan™ Optima Array uses the following QC metrics:
SNPQC greater than or equal to 8.5
MAPD less than or equal to 0.29
Waviness-SD less than or equal to 0.12

For CytoScan™ HD Suite and CytoScan™ 750K Suite, QC metrics have been fine-tuned for blood- derived constitutional samples. The SNPQC and Waviness-SD metrics are based on an assumption of a relatively normal diploid genome for which the majority of the genome is not mosaic. For cancer- related samples, the baseline assumption pertaining to constitutional samples is violated with regard to aberration frequency and high levels of mosaicism, which will likely trigger the SNPQC and Waviness-SD metrics to fail. Only the MAPD metric should be considered for non-constitutional samples. A failure of any one of these metrics for constitutional blood samples is a failure for that array result. There is no direct correlation between the absolute passing numeric value for any one of the metrics and the quality of a sample.

For CytoScan™ Optima Suite, QC metrics have been fine-tuned for amniocytes, chrionic villi, cultured cells, POC, and blood samples. The SNPQC and Waviness-SD are based on an assumption of a relatively normal diploid genome.

Answer Id: E13845

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Product FAQ

How do I learn more about the databases supported by the NetAffx™ Analysis Center?

Answer

Our Database Information Resource describes the functions and contents of the various databases used in the Analysis Center. Additionally, you can use the hyperlinks of the databases listed in the "top page" of the Analysis Center to obtain summaries of the databases.

Answer Id: E13461

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Product FAQ

How do I perform genotype trait association studies once I obtain genotype calls?

Answer

The output of the GTC is a text file that is compatible with multiple third-party software tools. Affymetrix™ works closely a number of GeneChip-compatible™ software providers that offer genome-wide linkage or association analysis solutions for Affymetrix™ genotyping arrays. GeneChip-compatible software providers that have been shown to support the genotype format for the Mouse Diversity Genotyping Array include:

- Golden Helix SNP & Variation Suite (SVS) - Golden Helix has tested data from the Mouse Diversity Genotyping Array and demonstrated compatibility. SVS can import SNP calls from the output text files through an automated import wizard. Once imported, data can be easily manipulated, augmented, and prepared with a full complement of QC tools, and then analyzed with powerful association methods, in-depth statistical analyses, and robust visualization tools. SVS can also import intensity data directly from the array’s CEL files, detecting changes in copy number and enabling CNV association studies. For more information, please visit www.goldenhelix.com or email info@goldenhelix.com.

- JMP™ Genomics from SAS - JMP Genomics can import text genotypes and annotation for the new array using the import individual text files process. Imported genotype text files should be transposed into standard JMP Genomics SNP format for downstream analysis (individuals in rows, SNPs in columns) using the transpose rectangular process. For more information, please visit www.jmp.com/software/genomics/ or email genomics@jmp.com.

- Partek™ Genomics Suite™ - Partek has tested sample data from the Mouse Diversity Genotyping Array and can import SNP calls from the output text files. Partek Genomics Suite supports single-marker association workflows as well as inheritance tests. For more information, please visit www.partek.com or email support@partek.com. Additional information about these and other GeneChip-compatible software providers can be found on our website.

Answer Id: E14160

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