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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

After installing Microarray Suite/GeneChip Analysis Suite, I am getting a message stating "Unable to load Microarray Suite component License Manager." Check that it is installed and registered correctly." How do I fix this?

Answer

The License Manager .dll file (gclm.dll) is probably not registered correctly. To correctly re-register the software:

-Verify that the options are set correctly in the "View" menu of Windows NT Explorer, in order to see the .dll files. Make sure you have "Show All Files" selected, and "Hide File Extensions..." un-selected; otherwise, you will not be able to see the file in the folder.
-Open Windows NT Explorer, locate the folder containing the Microarray Suite files, and find the gclm.dll file.
-Double-click the "gclm.dll" file to open the "Open With" menu.
-Click the "Other..." button to open the "Open With..." dialog box
-Find and double-click the "WinNT" folder, double-click the "System32" folder, select the "regsvr32.exe" file, and click the "Open" option.
-Click "OK".

If the procedure was successful, you will get a dialog box, informing you that the .dll has been successfully registered

Answer Id: E13624

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Product FAQ

Affymetrix Microarray Suite (MAS) is on the C: drive which is low on space. How can I create more room on the hard drive?

Answer

The library and data files can be moved to another drive, then deleted from the C: drive. After moving the files, remember to change your library file default settings in MAS to the appropriate directory by clicking on the Tools tab and then select Defaults in the drop-down menu, then File locations tab in the Defaults window.

Answer Id: E13625

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Product FAQ

What are masks?

Answer

Masks are rarely used features in MAS. There are three types of mask files:
-Image mask files: You may want to use an image mask if there is a large visible aberration on an image. You define the image mask based on the physical location of the image. Probe pairs included in the mask are excluded from the analysis. Image masks are associated with a given .dat/.cel file and cannot be used on other images.
-Probe mask files: Probe masks are defined by the probe set and probe pair number. Probe pairs included in this type of probe mask are excluded from the analysis when the probe mask is used. Probe masks can be applied across a data set.
-A second type of probe mask defines a select group of probe sets that can be used in normalization or scaling.

Answer Id: E13626

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Product FAQ

Why do you choose to use an rRNA-reduction strategy but not a poly-A mRNA-specific selection protocol?

Answer

It has been shown that a portion of the transcripts in total RNA do not necessarily contain Poly-A tails; therefore, they will be excluded by a poly-A RNA positive selection technique. The rRNA reduction approach will also make the protocol more robust in handling smaller amounts of total RNA samples as little as 1 μg.

Answer Id: E13644

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Product FAQ

If I realign the grid, how do I create a new .cel file?

Answer

If manual adjustment of the grid is necessary, the corresponding .cel file present at the time of adjustment will no longer be a valid representation of the realigned image data. Microarray Suite automatically detects this situation either on initial reopening of the readjusted .dat file or during the analysis process. Once the readjusted .dat file is opened, the .cel file is automatically created. The user does not need to carry out any overt steps to accomplish this.

Answer Id: E13627

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Product FAQ

Which GCOS features are not supported in Command Console Software?

Answer

Publishing and publish databases will not be supported. However, customers can leverage the flexibility of the file-based system to populate their own library information management systems (LIMS).
CHP data will be generated by separate Affymetrix and third-party applications, including Expression Console Software and Genotyping Console Software.
GeneArray 2500 and Fluidics Station FS400 instruments are not supported by Command Console Software.
Windows 2000 operating system is not supported.

Answer Id: E14228

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Product FAQ

What is the hybridization time for CytoScan 750K Arrays?

Answer

The hybridization time is 16 to 18 hours. If you have a limited number of fluidics stations, you can stagger the hybridization process by two hours. For example, if you have only one fluidics station and eight arrays, you can start the hybridization for four arrays at one time, and then start the hybridization for the other four arrays two hours later. After 16 hours, you can place the first four arrays on the fluidics station, and then place the next four arrays on the fluidics station two hours later. Thus, all eight samples will have hybridized for 16 hours. Another option is to wash the first set of samples at 16 hours and the second set at 18 hours.

We do not recommend staggering more than three wash/stain cycles in an 8-hour workday. Please consult your local Field Application Specialist for more details on the hybridization process.

Answer Id: E13919

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Product FAQ

What is the recommendation on how the total RNA samples should be prepared for the GeneChip Human Genome U133 Arrays?

Answer

A standard preparation method should be used, as recommended for the current GeneChip Human Genome U133 Arrays. The quality assessment metrics, including the Bioanalyzer trace and O.D. ratios, should remain unchanged.

Answer Id: E13645

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Product FAQ

How do I know if my first-cycle cDNA synthesis reaction has worked well?

Answer

It is challenging to assess the success of the cDNA synthesis reaction and this applies to both the One-Cycle and Two-Cycle protocol. This is because the amount of double-stranded cDNA obtained is quite small, and it is mixed in with the starting total RNA materials. The best way to QC this step is to carry out the subsequent IVT reaction and quantitate the cRNA yield. [This answer refers to a product that has been discontinued.]

Answer Id: E14368

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Product FAQ

How do I add additional probe sets in the .rpt file?

Answer

Use the Report Settings dialog on the short cut menu in Microarray Suite to open the Expression Report. You may add any probe sets desired by simply typing in the probe set name(s) you wish to add (this can also be accomplished by cutting and pasting from a text file). Keep in mind that the probe set name must be entered exactly as it appears in the analysis file, including the suffixes such as "12345_s_at".

Answer Id: E13628

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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

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Product FAQ

Are the Affymetrix Analysis Data Model (AADM) and Data Mining Tool (DMT) supported by Command Console Software?

Answer

AADM is a relational database model and is not supported by Command Console Software. Customers can access the Command Console indexer to get query capability. DMT is not supported by Command Console. Analysis capabilities similar to those in DMT are offered by various Affymetrix packages and by third-party GeneChip-Compatible (http://www.thermofisher.com/us/en/home/life-science/microarray-analysis/microarray-analysis-partners-programs/genechip-compatible-software-providers.html) packages.

Answer Id: E14229

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Product FAQ

I have never performed any small sample target labeling before. Do you have any suggestions for incorporating the Two-Cycle cDNA Synthesis Kit into our routine GeneChip microarray analysis?

Answer

The basic principles of the Two-Cycle Target Labeling Assay are very similar to the One-Cycle Standard Protocol, and many of the steps involved may look familiar. However, since it does require manipulation of very small amounts of materials in the 1st cycle, even the most experienced GeneChip microarray users may not obtain ideal data when using the Two-Cycle protocol the first time. Therefore, it is suggested that users first read the protocol very carefully, including all notes and tips, and then practice initially with diluted samples that you have previously characterized using the One-Cycle Standard Protocol. This way, you will be starting with materials of good quality and you already know what results to anticipate. Follow common laboratory practices that minimize RNase contamination and use caution at each step to prevent sample loss. [This answer refers to a product that has been discontinued.]

Answer Id: E14362

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Product FAQ

What is the hybridization temperature and rotation speed for the CytoScan 750K Array?

Answer

The hybridization temperature is 50 degrees C. The rotation speed is 60 rpm.

Answer Id: E13920

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