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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

Why can't I analyze Affymetrix data files stored on a CD?

Answer

Files in CD-ROM format are copied to the hard drive in read-only mode. MAS requires that this attribute be removed. To do this, open NT Explorer and select the file(s) you copied from the CD. Click the right mouse button and select Properties. Clear the Read-only check box near the bottom of the Properties screen and click OK.

Answer Id: E13523

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Product FAQ

How do the data compare with those obtained using the previous protocol when usign the Prokaryotic Traget Labeling Assay?

Answer

The data are highly similar with respect to basic array quality metrics including percent Present calls, background, noise, and Signal intensities. However, since the protocols differ in many areas, it is not recommended to compare the array data directly.

Answer Id: E13795

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Product FAQ

What is the detection sensitivity of the Two-Cycle cDNA Synthesis Kit protocol?

Answer

One way to assess the assay sensitivity is to monitor the global array metric of percent Present calls. From the same high-quality starting material, the Two-Cycle cDNA Synthesis protocol demonstrates highly comparable P% calls as the results generated from the One-Cycle cDNA Synthesis protocol. Another way to estimate the detection sensitivity is to use poly-A RNA spike-in controls. Following the recommended protocol included in the GeneChip Eukaryotic Poly-A RNA Control Kit, the Two-Cycle cDNA Synthesis Kit generally amplifies the samples sufficiently to detect the 3'-Probe Set of lys (the transcript with the lowest concentration, at 1:100,000 complexity ratio) as Present over 70% of the time. [This answer refers to a product that has been discontinued.]

Answer Id: E14365

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Product FAQ

How can the mismatch probe cell have a higher intensity than its corresponding perfect match probe cell?

Answer

There could be a number of reasons for this. It is possible that this probe sequence has high homology with another unknown sequence resulting in a high mismatch-to-perfect match ratio. Another possibility is a mutation or set of mutations in the sequence of the target transcript which causes specific binding to the Mismatch. Regardless of the cause, the built-in redundancy using multiple probe pairs to represent a single sequence on the probe array mitigates any significant impact on the final interpretation of the data.

Answer Id: E13524

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Product FAQ

For the CytoScan 750K Array, is it important to back up my data in ChAS?

Answer

Out of the five data files (ARR, AUDIT, DAT, CEL, CYCHP), it is important to backup and archive the ARR, CEL, and CYCHP file at a minimum. This will allow you to maintain the ability to either reanalyze from the CEL file, or re-visualize the results using the CYCHP file.

Answer Id: E13938

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Product FAQ

How do I analyze the data generated by the Axiom Genome-Wide BOS 1 Array Plate?

Answer

Genotyping Console (GTC) Software version 4.1 is used to analyze data from the Axiom Genome- Wide BOS 1 Array Plate. A guide (vignette) will be available that describes how to perform SNP filtering for quality control and normalization. This instructional document will be available at www.affymetrix.com/support/developer/powertools/changelog/VIGNETTE.html. Please look for the Axiom Genome-Wide BOS 1 APT Vignettes.

Supporting files are available to assist with SNP genotyping and can be found on www.thermofisher.com. The supporting files include:

- Sample genotyping script for APT
- CDF library file
- GeneChip Command Console Software (AGCC) library files
- Sample CEL (data) files and CEL file list
- Genotype and quality control (QC) sample output files
- Genotype and QC support files
- NetAffx Analysis Center annotation and alignment files

Answer Id: E14043

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Product FAQ

How many single nucleotide polymorphism (SNP) and copy number (CN) probes are included on the CytoScan HD Array?

Answer

CytoScan HD Array includes a total of approximately 6.5 million probes: 1 probe per allele in triplicate for 750,000 SNPs probes and 1.9 million non-polymorphic probes.

Answer Id: E13834

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Product FAQ

What are the internal grid lines on the array image for?

Answer

There is a new gridding algorithm in GCOS 1.3, specifically designed for image analysis of arrays with 5 μm or smaller feature size. This algorithm utilizes 169 subgrids (13x13) to address probe cells on the array. This method is superior to global gridding for arrays with feature pitch less than 11 μm.

Answer Id: E13660

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Product FAQ

Can I get access to comparison sample data of usage with the Prokaryotic Traget Labeling Assay?

Answer

Sample comparison .cel files are available from Affymetrix for customers to review that may help you through the transition. Please email techsupport@thermofisher.com for information about how to access the files.

Answer Id: E13796

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Product FAQ

What is the hybridization time using the FlashTag HSR labeling kit?

Answer

16 to 18 hours.

Answer Id: E14070

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Product FAQ

Which RNA isolation method do you recommend for the Two-Cycle cDNA Synthesis protocol?

Answer

Different tissue types may have different requirements for RNA extraction. Several commercial kits and protocols are currently available for total RNA isolation from small samples (tissues, biopsies, LCM samples, etc.). Select the one that is most suitable for the processing of your samples and follow the vendor-recommended procedures closely. Assess the quality and integrity of obtained total RNA samples carefully by gel electrophoresis or Bioanalyzer before starting the GeneChip target labeling protocol. [This answer refers to a product that has been discontinued.]

Answer Id: E14366

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Product FAQ

Which is greater, sample or assay variability?

Answer

Sample variability, which arises mainly from biological heterogeneity, is certainly higher than assay variability, and has been estimated to be at least 10-fold greater. We recommend that researchers run multiple samples per data point to account for sample-to-sample variability. In addition, carefully design the experiment in order to minimize potential variation associated with the samples.

Answer Id: E13525

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Product FAQ

How was the LD metric calculated with regard to breed for the Axiom Genome-Wide BOS 1 Array?

Answer

LD calculations were carried out for each breed separately.

Answer Id: E14035

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Product FAQ

What is CytoScan Cytogenetics Suite?

Answer

CytoScan Cytogenetics Suite consists of CytoScan arrays and CytoScan Reagent Kit, GeneChip Command Console Software (AGCC), and Chromosome Analysis Suite (ChAS). It enables the performance of high-resolution, genome-wide DNA copy number analysis and also provides genotyping information for the detection of copy neutral loss/absence of heterozygosity (LOH/AOH), which can be used to detect uniparental isodisomy (UPD). The combination of high-resolution DNA copy number data and the ability to detect gains, losses, and UPDs on a single array makes CytoScan Cytogenetics Suite ideal for cytogenetics studies.

Answer Id: E13939

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