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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

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

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

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

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

Why are the PLIER/RMA/MAS5 CHP files from Expression Console Software different than those produced by third-party software packages?

Answer

Two reasons explain why the numbers may be different between the two software applications. First, the development environment and compilers were different between the two software applications, resulting in minutely different behavior with floating point values. Secondly, the parameters used to call the algorithm may be different.

Answer Id: E14011

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Product FAQ

There are too many files showing in the file window in Microarray Suite. What can I do?

Answer

By placing files for projects in their own directories and changing the default settings for data in Microarray Suite appropriately, you can manage large numbers of files. In addition, with the Windows NT operating system, users can specify their own directory defaults in Microarray Suite while logging on and create their own directories for data. To do so, each user should have a unique logon name and organize files in subdirectories, for example, by project, user, date, or lab. Each user can then set the data default to a subdirectory of choice.

Answer Id: E13629

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Product FAQ

Does genomic DNA contamination in the sample interfere with the results, and how do I monitor the degree of its effect?

Answer

By titrating genomic DNA back into the total RNA samples and monitoring the deterioration of the array data, it was determined during development of the assay that a moderate amount of genomic DNA contamination will only have minimum effect on the array results. Therefore, routine RNA isolation techniques coupled with DNase treatment should yield sufficiently high-quality sample for analysis on the exon arrays.

Answer Id: E13646

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Product FAQ

What are the array QC metrics for the CytoScan arrays?

Answer

CytoScan HD and 750K arrays use the following QC metrics:
SNPQC greater than or equal to 15
MAPD less than or equal to 0.25
Waviness-SD less than or equal to 0.12

CytoScan Optima Array uses the following QC metrics:
SNPQC greater than or equal to 8.5
MAPD less than or equal to 0.29
Waviness-SD less than or equal to 0.12

For CytoScan HD Suite and CytoScan 750K Suite, QC metrics have been fine-tuned for blood- derived constitutional samples. The SNPQC and Waviness-SD metrics are based on an assumption of a relatively normal diploid genome for which the majority of the genome is not mosaic. For cancer- related samples, the baseline assumption pertaining to constitutional samples is violated with regard to aberration frequency and high levels of mosaicism, which will likely trigger the SNPQC and Waviness-SD metrics to fail. Only the MAPD metric should be considered for non-constitutional samples. A failure of any one of these metrics for constitutional blood samples is a failure for that array result. There is no direct correlation between the absolute passing numeric value for any one of the metrics and the quality of a sample.

For CytoScan Optima Suite, QC metrics have been fine-tuned for amniocytes, chrionic villi, cultured cells, POC, and blood samples. The SNPQC and Waviness-SD are based on an assumption of a relatively normal diploid genome.

Answer Id: E13845

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Product FAQ

Are individual genotypes generated from the CytoScan arrays?

Answer

Yes, genotypes can be generated in ChAS. The software uses BRLMM for genotyping, which uses a Bayesian model based on prior clusters. This product is not intended for genome-wide association studies.

Answer Id: E13998

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Product FAQ

For the CytoScan assay, does the PCR have to be set up in a separate pre-PCR clean room?

Answer

Using two separate rooms greatly reduces the risk of sample contamination by previously amplified PCR products. If only one room is available, designate one area of the room as the pre-PCR clean area and a separate area as the post-PCR clean area. If a one-room configuration is being used, it is highly recommended to use a laminar flow cabinet for the pre-PCR clean area. See the CytoScan Assay User Manual (Cat. No. 703038, https://tools.thermofisher.com/content/sfs/manuals/cytoscan_assay_user_manual.pdf) for more details about the recommended laboratory setup.

Answer Id: E13968

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Product FAQ

Do we have to use any Affymetrix Reagents with our assay?

Answer

GeneChip Hybridization Control Kit 30 reactions
GeneTitan Hybridization, Wash, and Stain Kit for miRNA Array Plates 96 reactions
GeneTitan Hybridization Module for miRNA Plates 96 reactions
Affymetrix FlashTag Biotin HSR RNA Labeling Kit 10 reactions
Affymetrix FlashTag Biotin HSR RNA Labeling Kit 30 reactions

Answer Id: E14203

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