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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

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

Can I analyze the results from my human, mouse, or rat transcriptome assays using GeneChip Operating Software (GCOS) or GeneChip Command Console Software (AGCC)?

Answer

Human, mouse, or rat transcriptome assays utilize an updated installer package that is not compatible with GCOS. Human, mouse, or rat transcriptome assays require AGCC for fluidics and scanning. The Expression Console Software is required to perform QC analysis of the human, mouse, or rat transcriptome array data. Expression Console Software can be downloaded at no charge from the website.

Answer Id: E14104

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Product FAQ

Will the SST-RMA algorithm be available for other array types, such as GeneChip Human Genome U133 Plus 2.0 Array?

Answer

No, the SST-RMA analysis algorithm will not be available in Expression Console Software for legacy array designs, due to vast amounts of publically available data. Customers who wish to take advantage of this analysis method for other array types should use SST-RMA with Affymetrix Power Tools (APT) software package.

Answer Id: E14022

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Product FAQ

What is the shelf life of the poly A kit?

Answer

At launch, the kit's shelf life is six months from the date of manufacturing. We will continue to perform real-time stability studies and anticipate extending the shelf life as we accumulate more real-time data.

Answer Id: E14377

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Product FAQ

Can the Genome-Wide Human SNP Array 6.0 be used for copy number analysis?

Answer

Yes. The combination of the SNP Array 6.0 and Genotyping Console 2.1 provides a great set of tools for researchers who would like to study copy number changes in cancer as well as copy number variation in association studies.

Answer Id: E13749

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Product FAQ

Which fluidics protocol should I use when processing human, mouse, or rat transcriptome assays?

Answer

FS450_0001 should be used when processing human, mouse, or rat transcriptome assays. Up-to-date fluidics scripts can be obtained from the website.

Answer Id: E14105

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Product FAQ

Which copy number workflows for the SNP Array 6.0 are supported in GTC 4.2?

Answer

GTC 4.2 can be used to perform the following copy number analyses for the SNP Array 6.0:

-Copy number (CN)
-Loss of heterozygosity (LOH)
-Copy number segment reporting
-Custom region copy number segment reporting

There are two options for copy number analysis workflows on the SNP Array 6.0:

-CN/LOH Reference Model File Creation and Analysis (Batch Sample Mode)
-CN/LOH Analysis with a Previously Created Reference Model File (Single Sample Mode)

Answer Id: E13689

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Product FAQ

Will SST-RMA be available in APT?

Answer

Yes, the SST-RMA analysis algorithm will be available in APT.

Answer Id: E14023

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Product FAQ

How do I evaluate the sensitivity and efficiency of the labeling reaction based on the Poly-A Controls?

Answer

First, examine the Present call rate of the 3' probe set of the poly-A RNA control transcripts. Following the recommended dilutions, all four poly-A RNA controls should be routinely called as Present in a Standard Assay. The poly-A RNA control present at the lowest concentration, lys, is expected to be called as Present >70-percent of the time for the Small Sample Target Labeling Assay vII, and the other three controls should be routinely called as Present.
Next, the relative Signal intensities of the four transcripts should also be checked such that they follow the same order of increasing poly-A RNA control concentration as expected. Example data can be found in the kit's package insert.

Answer Id: E14378

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Product FAQ

What is the nature of specificity of the probes included in the GeneChip Rat Expression Set 230?

Answer

The probes on the Rat 230 are designed to detect an anti-sense target prepared by the Affymetrix 3' biased assay, and these probes are annotated with the "_at" extension. The primary goal in probe selection is to select a probe set unique to single transcript or common among multiple transcripts from the same gene.

Often it is not possible to select a probe set that is unique to a single transcript because multiple transcript variants share common sequence. Such probe sets have the "_s" extension. Occasionally, it is not possible to select a unique or shared probe set. Such probe sets have the "_x" extension.

For more information, please review the "_s" and "_x" probe set descriptions.

Please note: There are no "_f", "_g", "_r", "_i", or "_n" probe sets in the Rat Expression Set 230 design opposed to the RG-U34 design. This is because the non-unique probe set types were simplified and adjusted to account for improvements to the probe selection rules.

Answer Id: E13806

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Product FAQ

One of my hybridizations results in skewed values for several of the metrics, but the values aren’t grossly out of line. I could make a case to keep it in or discard it. What should I do?

Answer

If a sample appears “on the line,” it is best to leave the sample in the experiment for analysis and simply flag it as questionable. During the initial analysis, treat all samples uniformly. Once candidate genes have been identified, review how the questionable sample changes data relative to the other replicates within the sample. It is always possible to remove a sample later in the analysis workflows.

Answer Id: E14030

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Product FAQ

What is the difference between GeneChip Human Transcriptome Array v1(HTAv1) and GeneChip Human Transcriptome Array 2.0 (HTA 2.0)?

Answer

HTAv1, also known as Glue Grant Human Transcriptome Array (GG-H), is a custom array made in collaboration with Stanford Genome Technology, Wing Wong's lab at Stanford, and the Inflammation and Host Response to Injury program (“Glue Grant”). The array was designed to interrogate gene expression, alternative splicing, detection of coding SNPs and non-coding transcription. Permissions from the group are required to use this array. HTA 2.0 is one of our catalog arrays. This array follows a similar design as the HTAv1 but focus on the whole transcript gene expression and alternative splicing of coding and non-coding transcripts. We provide assay and software for the processing and analysis of this array.

Answer Id: E14346

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Product FAQ

What is the array format for the Genome-Wide Human SNP Array 6.0?

Answer

49 format, 5 µm Feature Size

All the SNPs are tiled with PM only 3-4 replicated probe pairs per SNP.

Answer Id: E13751

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Product FAQ

What format are the human, mouse, or rat transcriptome arrays?

Answer

Human, mouse, or rat transcriptome arrays are 49-format.

Answer Id: E14106

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