You searched for: 

genechip products

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

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Using the sub-cluster databanks, how can I determine if my favorite sequence was used for probe selection?

Answer

Obtain the accession number for your gene of interest from a public database - such as UniGene, GenBank, or dbEST-and query the corresponding sub-cluster databanks in the NetAffx Analysis Center. You may also perform a sequence alignment of your favorite gene with Affymetrix probe sequences, using the Probe Match tool. Learn more about the Probe Match tool (https://tools.thermofisher.com/content/sfs/manuals/probematch_manual.pdf).

Answer Id: E13475

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Can I start using the new 3' IVT Express Kit right away, even in the middle of my experiment?

Answer

We would recommend completing any current project with the same labeling method that you have been using. Although concordance is quite high between the kits, it is best to continue with one labeling method in any experiment. [This answer refers to a product that has been discontinued.]

Answer Id: E14348

Was this answer helpful?

Yes
No
Thank you for your response

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

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Are there any circumstances in which I would benefit from using RMA over SST-RMA with human and mouse transcriptome arrays?

Answer

Users will benefit from using the SST-RMA when comparing data (significantly changed gene lists) with those processed using the RMA summarization only.

Answer Id: E14018

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Are the data obtained following the Small Sample Target Labeling vII (SSTLvII) comparable to those obtained using the Two-Cycle cDNA Synthesis Kit?

Answer

The array results are highly comparable with respect to cRNA length and yield, Percent Present call rate, Signal intensity value, 3'/5' ratios, false change analysis, and poly-A RNA control spike performance. However, since the protocol has been modified (see detail below), it is recommended NOT to compare data obtained from the two protocols directly. [This answer refers to a product that has been discontinued.]

Answer Id: E14359

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Can I use less than 50ng of Total RNA as input with the 3' IVT Express Kit?

Answer

Yes, for some RNAs it may be possible to generate sufficient labeled aRNA with less than 50ng input (particularly for smaller array formats with lower aRNA requirements). However, lower input amounts have not been rigorously tested during development and therefore, we cannot guarantee array performance. [This answer refers to a product that has been discontinued.]

Answer Id: E14349

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

The recommended starting amount of total RNA for the One-Cycle protocol has been reduced from 5 µg to 1 µg. Do you have any data to support that the procedure works well with the reduced amount of starting material?

Answer

Studies were conducted in-house to compare the data obtained from 1 µg vs. 5 µg of starting total RNA, and the array results were highly concordant with respect to detection sensitivity (percent Present call) and reproducibility (Signal correlation, Absolute Call concordance). However, subtle differences were observed. Therefore, for best comparability of results, it is generally recommended to use the same amount of starting RNA in studies where the data are intended to be directly compared.

Answer Id: E13613

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What if I need to share GCOS files with my coworkers?

Answer

GCOS users can use the import and export functions to accomplish the task. Alternatively, in a client-server configuration, researchers can directly access data and experiment information from the server database.

Answer Id: E13561

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What algorithm(s) can be used to make copy number calls?

Answer

We recommend the TuScan algorithm. This algorithm has fixed settings based on 19 probes/call to ensure high sensitivity and specificity at the stated resolution claims. Nexus Express Software for OncoScan FFPE Assay Kit has an additional algorithm for copy number calls from OncoScan FFPE Assay Kit: SNPFASST2 algorithm, developed and supported by BioDiscovery. This allows the user to adjust settings and make custom calls (e.g., with fewer probes). Use cases are:
When breakpoints are clear with fewer probes
When probe re-centering is needed

Answer Id: E13857

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Are there any service providers for the Mouse Diversity Genotyping Array?

Answer

A number of service providers have experience running the SNP 5.0/6.0 assay and the genotyping call algorithm that is used with the Mouse Diversity Genotyping Array. The list includes The Jackson Laboratory, the microarray and computational analysis group that participated in the design and validation of the Mouse Diversity Genotyping Array. The Jackson Laboratory has experience assaying more than 1,000 samples, has access to the most up-to-date methods, and has achieved excellent genotyping call accuracy. Their service spans basic delivery of raw data and genotype calls to custom bioinformatics analysis. For more information, please visit their website or email jaxservices@jax.org.

Answer Id: E14166

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

How do I cite the NetAffx Analysis Center in a publication?

Answer

When citing the NetAffx Analysis Center, please refer to: Liu G, Loraine AE, Shigeta R, Cline M, Cheng J, Valmeekam V, Sun S, Kulp D, Siani-Rose MA. NetAffx: Affymetrix probesets and annotations. Nucleic Acids Res. 2003;31(1):82-6.

Answer Id: E13477

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Are there any specific concerns for running FlashTag HSR labeling?

Answer

All materials (tubes, tips, etc.) should be nuclease-free, and all reagents should be prepared with nuclease-free components.

Answer Id: E14067

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What can I expect to see with SST-RMA compared to RMA?

Answer

When filtering by fold change cutoffs, expect a larger number of differentially expressed genes compared to the standalone RMA. When comparing the number of differentially expressed genes (defined by fold change filters) to other methods, such as RT-PCR and RNA-Seq, expect this number to align more with these methods when using GCCN-SST. There is no impact on sensitivity or specificity of data. SST-RMA was designed to address comparability to other technologies. The same experimental design recommendations still apply when designing an expression study with microarrays.

Answer Id: E14019

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Must GCOS be uninstalled in order to install Command Console Software?

Answer

No.

Answer Id: E14231

Was this answer helpful?

Yes
No
Thank you for your response