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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 are the quality requirements for genomic DNA for a successful run on a CytoScan XON array?

Answer

Sample must be double-stranded genomic DNA (gDNA) that is not degraded (size 10 kb by gel analysis), not contaminated, and free of PCR inhibitors. Sample should be diluted to 20 ng/µL in low-EDTA TE buffer.

 

Answer Id: E16631

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Product FAQ

Are the equipment requirements for running the CytoScan XON assay different from the CytoScan assay?

Answer

Consumable and equipment requirements are the same for running both the CytoScan XON assay and the CytoScan assay.

   

Answer Id: E16632

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Product FAQ

What are the recommended OD 260:280 ratios for input RNA for downstream array analysis with miRNA GeneChip microarrays?

Answer

We do not have a specific recommendation. A high-quality RNA sample will have a ratio of at least 1.95. However, if microRNAs are present in samples with lower 260:280 ratios, these samples can still be used.

Answer Id: E14055

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Product FAQ

Why doesn't the Zip study utility always include the library CHP files when requested?

Answer

The Zip utility only includes library files for exon arrays when CHP files are analyzed as part of the study. If the user creates a study and adds existing CHP files, then the library files will not be included in the Zip archive. To add the appropriate library files, identify them through the CHP file properties in Expression Console Software and then manually add them to the Zip archive

Answer Id: E14013

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Product FAQ

Which version of Chromosome Analysis Suite (ChAS) Software is required to analyze CytoScan XON arrays?

Answer

Chromosome Analysis Suite (ChAS) Software version 3.3 is required to analyze CytoScan XON arrays.

 

Answer Id: E16633

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Product FAQ

Why can I not see the miRBase identifier for probe sets in Affymetrix Expression Console Software charts and graphs?

Answer

We have changed the naming convention for probe sets on our miRNA arrays to be consistent with other array designs. Probe set IDs on Affymetrix miRNA 4.0 and 4.1 Arrays (and newer) will be a unique number. The probe set name will have the accession number and an Affymetrix suffix (e.g., “_st”). While the transcript ID is no longer contained in the probe set name, it is included in the annotation file.

Answer Id: E14122

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Product FAQ

Can I use FFPE total RNA samples for FlashTag labeling?

Answer

Yes, as long as the FFPE sample contains microRNA. Regardless of the degradation of the FFPE total RNA, use an ATP dilution of 1:500.

Answer Id: E14056

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Product FAQ

What are the hardware and software requirements for Command Console Software?

Answer

1GB of RAM (2GB Recommended)
500 GB hard disk space (for data storage)
3 GHz Pentium 4
Windows XP sp3 for instrument control install
Windows XP sp3 or Windows Vista for data analysis install
Internet Explorer 6.0 sp2 or Firefox 2.0

Answer Id: E14265

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Product FAQ

What is the difference between NetAffx library files and those downloaded from your website?

Answer

There is no difference. The library files downloaded from NetAffx are not installed and registered with GCOS, but they are exactly the same files.

Answer Id: E14014

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Product FAQ

What are the features of GCOS and GCOS Server?

Answer

Please see the features below for MAS, GCOS Client, or GCOS Server:

Instrument Control / Data Acquisition +, +, -
Gene Expression Data Analysis (Statistical Algorithm (CHP) +, + ,+
Manage & Associate Projects, Experiments, Samples & Data -, +, +
Publishing to AADM Database -, +, +
MIAME Standard Template -, +, +
Barcode Support, Automation -, +, ++
User Access, Roles, Security -, -, +
Centralized Data Sharing -, -, +

Answer Id: E14175

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Product FAQ

How does the Genome-Wide Human SNP Array 6.0 assay work?

Answer

DNA is digested with Nsp I and Sty I restriction enzymes and ligated to adaptors that recognize the cohesive four base pair (bp) overhangs. All fragments resulting from restriction enzyme digestion, regardless of size, are substrates for adaptor ligation. A generic primer that recognizes the adaptor sequence is used to amplify adaptor-ligated DNA fragments. PCR conditions have been optimized to preferentially amplify fragments in the 200 to 1,100 bp size range. PCR amplification products for each restriction enzyme digest are combined and purified using activated beads. The amplified DNA is then fragmented, labeled, and hybridized to a Genome-Wide Human SNP 6.0 Array.

Answer Id: E13761

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Product FAQ

What effect does SST-RMA have on alternative splicing events as defined in Transcriptome Analysis Console (TAC) Software?

Answer

With SST-RMA, more significant changes are observed in the number of expressed genes with alternatively spliced events compared to RMA.

Answer Id: E14020

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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

Why are there more data headers and columns in my miRNA 4.0/4.1 or newer annotation files?

Answer

The miRNA 4.0/4.1 annotations contain additional data fields to help ease the integration and correlation of small non-coding RNA data contained on Affymetrix miRNA 4.0 and 4.1 Arrays (and newer) with the content from our other expression products such as GeneChip Human Genome U133 Plus 2.0 Array, GeneChip Human Gene 2.0 ST Array, and GeneChip Human Transcriptome Array 2.0. These additional fields include:

- Genomic context (where the miRNA is located in the genome)
- Clustered miRNA (miRNA that are located 10 KB from one another)
- Predicted miRNA targets
- Validated miRNA targets

Answer Id: E14123

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Product FAQ

How important is it to evaluate the value of the Scaling Factor between different GeneChip arrays?

Answer

Scaling Factor is the multiplication factor applied to each Signal value on an array. A Scaling Factor of 1.0 indicates that the average array intensity is equal to the Target Intensity. Scaling Factors will vary across different samples and there are no set guidelines for any particular sample type. However, if they differ by too much within a set of experiments, approximately 3-fold or more, this indicates wide variation in the .dat files. Therefore, the analyzed data (in the .chp file) should be treated with caution.

Answer Id: E13521

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Product FAQ

Are there any updates to algorithm(s) in ChAS 3.1?

Answer

Yes, we have updated the cyto (CytoScan copy number) single-sample analysis engine with non- diploid analysis and correction. We have also converted the engine to make use of the APT2 analysis framework. The APT2 framework provides support for higher-precision internal calculations for the implementation of new algorithms, such as normal diploid correction, and for other future improvements.

Answer Id: E13888

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Product FAQ

What has been used as reference RNA for FlashTag labeling?

Answer

Ambion FirstChoice Total RNA samples have been used as reference RNA.

Answer Id: E14057

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Product FAQ

Are there any software packages that are not compatible with Command Console Software?

Answer

Affymetrix software applications have been updated to work with Command Console Software, including Expression Console Software, Genotyping Console Software, DMET Console Software, Targeted Genotyping Analysis Software (GTGS), Sequence Analysis Software (GSEQ), and Tiling Analysis Software (TAS). Some legacy tools do not work with Command Console files and require conversion back to GCOS file formats, such as the Copy Number Analysis Tool (CNAT). Note: No other web servers can be installed on the Command Console workstation. Other web servers will conflict with the Command Console web server.

Answer Id: E14266

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Product FAQ

How do I link directly (deep link) to Probe Set Annotation summaries in the NetAffx Analysis Center?

Answer

You can now link directly to NetAffx probe set summaries from within your own applications or websites using a convenient deep link URL.
To link to information for individual probe sets, use the following URL format:
https://www.affymetrix.com/LinkServlet?array=&probeset=
To link to information for a list of probe sets, use the following URL format:
https://www.affymetrix.com/LinkServlet?array=&probeset=
Detailed Information:
For details on the valid values of the ARRAYNAME and PROBESET parameters, please refer to the Direct Access To Probe Set Information Manual
Examples of Deep Links:
https://www.affymetrix.com/LinkServlet?probeset=10156_at
https://www.affymetrix.com/LinkServlet?array=U74&probeset=129277_at
https://www.affymetrix.com/LinkServlet?array=U95&probeset=1000_at
https://www.affymetrix.com/LinkServlet?probeset=1000_at,1002_f_at,38996_at

Answer Id: E13476

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Product FAQ

I added my exon library files to my library folder, but the application still will not analyze exon arrays. What should I do?

Answer

Examine the messages in the status window to identify the missing library files in Expression Console Software. If the computer is connected to the internet, use the download library files functionality to add the necessary files. In addition to these files, Expression Console Software requires two additional files for exon analysis: the qcc file ith control probe information and an exon_analysis_configuration file.

These files are automatically included when Expression Console Software is used to download the library files; however, if you manally add file to Expression Console Software, you will need to obtain the qcc and exon_analysis_configuration files from www.thermofisher.com.

Answer Id: E14015

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Product FAQ

How long does the GeneChip eukaryotic expression assay take from sample preparation to obtaining the array image?

Answer

There is some variation in processing time depending on sample type and array type, however, in general, starting from total or poly-A mRNA, the entire GeneChip eukaryotic expression assay take approximately 2 1/2 days (assuming 8 hrs in a day). Target labeling takes approximately 2 days, followed by overnight hybridization to a GeneChip expression array. Washing and staining takes approximately 1 hr and 15 mins, and scanning varies from 10-35 mins.

Answer Id: E13585

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Product FAQ

What about data compatibility between MAS v.5.1 and GCOS v.1?

Answer

We have maintained full forward and backward data compatibility between GCOS v.1 and MAS v.5.1. The following summarizes file compatibility between the two software products.

MASGCOS ClientGTYPE/GSEQ
Create:Create:Create:
DATDATCHP (DNA analysis)
CELCELFASTA
CHPCHP (expression)
EXPCAB (export)
RPT, TXTRPT, TXT (export)
Analyze:Analyze:Analyze:
DATDATCEL (GCOS)
CELCEL

Answer Id: E14176

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Product FAQ

I can see the gene descriptions when I am logged on to the system with administrative rights, but I cannot see them when I am logged on as a normal user. How do I fix this?

Answer

This situation is most likely a permissions issue with the SQL Database. At the Start menu, open the Run menu, and run "regedt32". Once in the regedt32 window, select the "Software" option, then select "Affymetrix", "GeneChip", and "Database". With "Database" highlighted, select "Permissions" from the "Security" menu. Double-click on the user name, and select "Full Control (All)".

Answer Id: E13618

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Product FAQ

Can I export my data in text format?

Answer

Yes. With ChAS 3.1 and above, you can now export table data in word (docx), pdf, text, or transfer to clipboard. You can export graphic view data in pdf, docx, and png formats.

Answer Id: E13874

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Product FAQ

What is the recommended number of samples to cluster when using the Birdseed v1 algorithm with the SNP 6.0 assay?

Answer

The recommended number of samples that should be clustered and analyzed using the Birdseed v1 algorithm is a minimum of 44. A minimum of 15 female samples should be included for robust gender determination results.

Answer Id: E13762

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Product FAQ

Will the QC controls look different in Expression Console Software with GCCN-SST RMA?

Answer

The Relative Log Expression (RLE) boxplots are the only controls that might look different in Expression Console Software.

Answer Id: E14021

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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

Which assay do you recommend for use with Affymetrix GeneChip miRNA Arrays?

Answer

Affymetrix only supports use of the Affymetrix FlashTag Biotin HSR RNA Labeling Kit for preparing targets to be applied to GeneChip miRNA Array, Affymetrix miRNA Array Strip, and Affymetrix miRNA Array Plate. This product may be ordered through Affymetrix using Cat. No.s 901910 for the 10- reaction kit and 901911 for the 30-reaction kit.

Answer Id: E14124

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Product FAQ

Is there a way to check for successful labeling prior to array hybridization?

Answer

Successful biotin labeling is verified via a simple colorimetric ELOSA assay through the hybridization of the biotin-labeled RNA Spike Control Oligos (Vial 8) to complementary ELOSA Spotting Oligos (Vial 9) immobilized onto microtiter plate wells. Refer to Appendix A of the manual.

Answer Id: E14074

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