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

Can I install ChAS 3.1 on my AGCC workstation computer?

Answer

Due to the amount of memory that ChAS 3.1 needs to operate, Affymetrix™ VERY STRONGLY recommends that you DO NOT install the ChAS 3.1 on production AGCC computers being used for scanning and operating fluidics systems.

Answer Id: E13870

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What versions of NetAffx™ analysis files are compatible with ChAS 3.1?

Answer

NA33 (Hg19) is only compatible in ChAS 3.1. ChAS 3.1 automatically prevents you from selecting an incompatible NetAffx™ analysis file version for analysis or when viewing analysis results.

Answer Id: E13871

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Can I open two files that have been analyzed with different NetAffx™ versions at the same time in the ChAS 3.1 browser?

Answer

The ChAS 3.1 browser allows for loading of different NetAffx versions at the same time (only if the versions are from all the same reference and genome builds).

The ChAS 3.1 browser cannot load NetAffx versions from different genome builds (Hg18 and Hg19) or from an external reference version (dbSNP build 135 and dbSNP build 132).

Answer Id: E13872

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What is Mendelian error check? Is it available for all arrays?

Answer

The Mendelian error check analysis provides two key points of information:

-Are the input samples related (e.g., mother-child, father-child)?
-Do any chromosomes have an elevated occurrence of Mendelian errors?
The Mendelian error checking feature is for CytoScan™ arrays only.

Answer Id: E13873

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Can I export my data in text format?

Answer

Yes. With ChAS 3.1, 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

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

With the new algorithm, do I need to make new reference model files for analysis?

Answer

While the reference model algorithm is unchanged, there are differences in file format used for reference model files. The reference model files provided by Affymetrix™ have been updated to work with ChAS 3.1. Users generating their own reference model file will need to regenerate the model file in ChAS 3.1 to be able to use it.

Answer Id: E13890

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

How can I export allelic difference, smooth signal, log ratio, and other probe-level data?

Answer

For a whole chromosome or a region, go to the Graphs tab in ChAS 3.1 and use the “copy to clipboard” or “export to txt” functions.

For the whole genome, using ChAS 2.1 or later versions, go to the analysis manager/analysis dashboard and select the “QC results” tab. Then open and/or select the file(s) to export, press the “Generate Report” button, and select the “Export probe level data function.” Data will be exported in .txt format.

Answer Id: E13875

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Are there any specific recommendations on the use of the ChAS 3.0 database?

Answer

Loading samples with a high number of segments may cause performance to be slower when publishing or promoting mosaic segments. Using “edit mode” and “fusing” fragmented segments before uploading is highly recommended.

Answer Id: E13891

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What are the key benefits of Command Console Software?

Answer

Command Console Software is file based, which means that users can:
Manage their files with industry-standard tools
Share and move data by simply moving files
Rename data files

There are multiple ways to register samples, including batch registration through tab-delimited spreadsheets. Users can custom define sample attributes to precisely capture sample annotations and experimental metadata.

Answer Id: E14213

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What are the recommended graph settings for data interpretation in ChAS 3.1?

Answer

We recommend changing the weighted log2 ratio graph from the default setting to minimum at -1.5 to maximum at 1.5, using data type as points. We recommend changing the allele peaks graph from the default setting to minimum at -2 to maximum at 2, using data type as points. The other graphs can stay at the default values.

Answer Id: E13876

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What are the stopping points in the CytoScan™ Assay?

Answer

After any stage in the assay (including fragmentation) you can store the samples at -20 degrees C if you are not proceeding directly to the next step. However, once you have initiated a stage, you must complete it before storage of the samples.

Answer Id: E13908

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

How do I upgrade the ChAS 3.0 database to the ChAS 3.1 database?

Answer

During the installation of ChAS 3.1 on a system with ChAS 3.0, the database will automatically be updated to the current ChAS 3.1 version. Older backup database files can still be updated to ChAS 3.1 during the restore process. Please see the ChAS 3.1 User Guide for instructions on how to restore a backup file.

Answer Id: E13892

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

How will Command Console Software improve data management?

Answer

Data sharing: Command Console Software is a file-based system, making sharing data as simple as copying and pasting.
Data search and filtering: Command Console Software includes a file index and a user interface for querying data files on any attribute. This allows the user to search on any system- or user-entered value.
Backup: Command Console data files can be backed up with any industry-standard file backup utility. No specialized skill sets are required and Command Console Software does not use a database that would require backup or maintenance. Simply back up the files in the Command Console application and data root directories.
Storage: Command Console Software supports flexible storage options for data files. More information will be discussed in upcoming web seminars.

Answer Id: E14214

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Which genotype is presented in each allele peak track?

Answer

AA markers would be distributed about +1.
AB markers would be distributed about 0.
BB markers would be distributed about -1.

Answer Id: E13877

Was this answer helpful?

Yes
No
Thank you for your response