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

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

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What is the correct fluidics script for the Clariom S (human, mouse and rat) array?

Answer

The Clariom S array is a 400 format, the correct script is FS450_0007.

Answer Id: E14311

Was this answer helpful?

Yes
No
Thank you for your response

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

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What are the available assay options for running the Clariom S array?

Answer

Depending on input, sample type, and platform, you have several options:
Cartridge: Assays for 100 pg-50 ng of total RNA isolated from whole blood, cultured cells, and fresh/fresh frozen or FFPE tissues.
Pico Assay Assays for 50-500 ng of total RNA isolated from whole blood, cultured cells, and fresh/fresh frozen tissues.
WT Plus Assay Plates: Assays for 100 pg-50 ng of total RNA isolated from whole blood, cultured cells, and fresh/fresh frozen or FFPE tissues for analysis on GeneTitan Instrument.
Pico Assay HT Assays for 50-500 ng of total RNA isolated from whole blood, cultured cells, and fresh/fresh frozen tissues for analysis on GeneTitan Instrument.

Answer Id: E14312

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What are the library files for Command Console Software?

Answer

Media file - contains information about the media type on which the array is printed, such as a cartridge or 96-well plate.
Master file - contains array-specific design information and replaces the cif file. It also identifies the analysis library file packages and scan parameter files.
Workflow file - lists the actions to be performed on each probe array type, such as gridding and CEL file generation. The file also includes references to the appropriate algorithm parameter file.
Algorithm parameter file - contains the parameters for an algorithm.

Answer Id: E14241

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

Product FAQ

Is globin reduction of blood samples required when using the Clariom S arrays?

Answer

No, there is no need to globin reduce your samples prior to starting the assay for the Clariom S array.

Answer Id: E14313

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Will SST-RMA be available in APT?

Answer

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

Answer Id: E14023

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Where can users learn more about the workflow or specific steps or features in the Command Console software?

Answer

Please visit the training and tutorials section (www.thermofisher.com/us/en/home/life-science/microarray-analysis/microarray-analysis-learning-center/microarray-analysis-training.html) of the website for additional information.

Answer Id: E14242

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Will the data be identical when generated from Command Console Software versus GCOS?

Answer

Command Console Software is not guaranteed to produce results identical to GCOS.

Answer Id: E14232

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What are the Clariom Assay scan times and file sizes?

Answer

Clariom D Assay - scan time is about 33 min.
- DAT file size about 790-800MB
- CEL file size about 68 MB

The Clariom S - scan time is about 5 min.
- DAT file size about 35-40MB
- CEL file size about 3 MB

Answer Id: E14314

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

How are DAT files gridded and/or re-gridded manually?

Answer

This functionality is supplied through the Command Console Viewer. Please see demo in the training and tutorials (www.thermofisher.com/us/en/home/life-science/microarray-analysis/microarray-analysis-learning-center/microarray-analysis-training.html) section of the website.

Answer Id: E14249

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

When should data analyzed with RMA be re-analyzed using SST-RMA?

Answer

You should re-analyze your data if comparing with RT-PCR or RNA-Seq data using fold change values for filtering.

Answer Id: E14024

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What file sizes are associated with the CytoScan 750K Array?

Answer

The CEL file is ~46 MB, and the CYCHP file is ~33 MB.

Answer Id: E13930

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

In the Command Console Software, what is sample/array registration?

Answer

It is the process of associating a sample record to a physical array or set of physical arrays. With this feature, users can link a sample to a single array, a sample to an array set (such as the GeneChip HG-U133A and B Arrays, or the GeneChip Human Mapping 500K Array Set), or a sample to an array type in replicate (one sample run on multiple arrays of the same type).

Answer Id: E14243

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What is the threshold for the Contrast QC metric for the SNP Array 6.0?

Answer

The Contrast QC threshold is 0.4 or greater. The overall quality of the data set is assessed by measuring the average Contrast QC for all passing samples. The average Contrast QC for all passing samples should be 1.7 or greater.

Answer Id: E13680

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

I would like to check my miRNA Array data with qRT-PCR. In addition to my miRs of interest, what other qRT-PCR controls should I run?

Answer

At least 5 miRs or SnoRNAs should be used to normalize:

RU44, RU48, and/or U6 microRNAs that are not changed among your samples, and are at least 5X over background, according to your microarrays. These miRs might include miR 15,16, 17, or let 7a, let 7b, let7c

All 5 (or more) of these RNAs should not show any change among the samples. Average some or all of these to get the normalization factor, and apply to your qRT-PCR data.

Answer Id: E14093

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Where can I learn more about Command Console Software?

Answer

You can learn more about the Command Console Software through:
Training & tutorials - web tutorials
Upcoming web talk series
Contacting your local support representative
User documentation

Answer Id: E14233

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

How big are the .dat and .cel GeneChip Exon Array files?

Answer

The .dat files are approximately 750 MB in size, and the binary .cel files are approximately 60 MB in size.

Answer Id: E13528

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

How many freeze/thaw cycles have been validated for use with the GeneChip HT 3' IVT PLUS assay?

Answer

We guarantee up to three freeze/thaws.

Answer Id: E14315

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

How many genes and transcripts are represented on the GeneChip Rat Expression Set 230?

Answer

The Rat Expression Set 230, consisting of two GeneChip arrays, contains over 31,000 probe sets representing more than 30,200 transcripts and variants, including over 28,000 well substantiated rat genes.

Answer Id: E13800

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

When is array registration necessary?

Answer

Array registration is not required to process the physical array through the Fluidics Station and scanner.

Answer Id: E14250

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Error when exporting in VCF format in Axiom Analysis Suite, there is no genotyping information in the exported file. Instead of genotypes there is only "./." for all samples on all SNPs. What should I do?

Answer

In order to export in VCF format from the Axiom Analysis Suite, the annotation files need to have the ref and alt allele columns. If these columns are blank in the annotations, the software will export "./." in place of genotypes.

Answer Id: E14330

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What are the positive and negative controls?

Answer

Positive controls are probe sets designed against putative exons of about 100 housekeeping genes shown to be expressed at detectable levels across a variety of tissues. Since the extent of alternative splicing and transcript expression is not known for all tissues, not all exons are expected to be expressed in all tissues.

Negative controls are putative introns of the same 100 housekeeping genes chosen for positive controls. These probe sets may be expressed in certain tissues through intron retention. They are not true negative controls. Overall, the positive and negative control probe sets provide a medium-size dataset with expected high and low signal values, respectively. This data set is useful to estimate overall data quality though the Pos_vs_neg_auc value.

Answer Id: E14025

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Where are the microarray annotation and sequence files for download?

Answer

The annotation and sequence files contain the complete entries for all probe sets on the array, taken from the NetAffx Analysis Center. They are intended to be used primarily in spreadsheet applications and database programs (such as SQL databases). Interactive and Batch queries can be performed in the NetAffx Analysis Center to find information for individual probe sets of interest. Annotation files are available for most Affymetrix GeneChip Arrays.

Please select your array of interest.
MAGE-ML XML Annotations
Manual, Probe Set Data in MAGE-ML Format (https://tools.thermofisher.com/content/sfs/manuals/netaffx_MAGE_ML_manual.pdf)
CSV Annotations
Manual, Probe Set Data in Tabular Format (https://tools.thermofisher.com/content/sfs/manuals/taf_manual.pdf)
Alignments
Manual, Alignments to Genome in PSL Format (https://tools.thermofisher.com/content/sfs/manuals/alignments_psl_manual.pdf)

Answer Id: E13478

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What are the proper storage conditions for Affymetrix miRNA Array Plates?

Answer

The array plates should be stored at 2-8 degrees C.

Answer Id: E14116

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

If I suspect my gDNA requires further purification when using an Axiom array, what is the recommended cleanup protocol?

Answer

If gDNA preparation is suspected to contain inhibitors, the following cleanup procedure can be used:
1. Add 0.5 volumes of 7.5 M NH4OAc, 2.5 volumes of absolute ethanol (stored at -20 degrees C), to gDNA.
2. Vortex and incubate at -20 degrees C for 1 hr.
3. Centrifuge at 12,000 x g in a microcentrifuge at room temperature for 20 min.
4. Remove supernatant and wash pellet with 80% ethanol.
5. Centrifuge at 12,000 x g at room temperature for 5 min.
6. Remove the 80% ethanol and repeat the 80% ethanol wash one more time.
7. Resuspend the pellet in reduced EDTA TE Buffer (10 mM Tris-HCl pH 8.0, 0.1 mM EDTA).

Answer Id: E14286

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What software is available for genotyping and copy number analysis?

Answer

All genotyping and copy number analysis is performed with the Chromosome Analysis Suite (ChAS) Software v.1.2 or higher (http://www.thermofisher.com/us/en/home/life-science/microarray-analysis/microarray-analysis-instruments-software-services/microarray-analysis-software/chromosome-analysis-suite.html). Additionally, there is an update installer to install the 750K-specific files. That installer is downloadable from the website and is named “CytoScan750K_ChASSupportUpdate.exe”. This product is not intended for genome-wide association studies.

Answer Id: E13931

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Can arrays be registered in batches in the Command Console Software?

Answer

Yes. Please see the demonstration in the training and tutorials (www.thermofisher.com/us/en/home/life-science/microarray-analysis/microarray-analysis-learning-center/microarray-analysis-training.html) section of the website for additional information.

Answer Id: E14244

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What are the thresholds for the QC Call Rate metric?

Answer

The QC Call Rate threshold is 86 percent or greater for the SNP Array 5.0, 93 percent or greater for the 500K Array Set, and 95 percent or greater for the 100K Set. In good-quality data sets, 90 percent of samples should pass the QC Call Rate threshold and the average QC Call Rate should be in the mid-90 percent range. Occasionally, poor samples will pass the QC Call Rate metric, which is why Contrast QC is recommended for the SNP Array 6.0. To minimize the risk of poor samples passing the QC Call Rate metric, samples with outlier values for heterozygosity or Birdseed call rate should be rejected.

Answer Id: E13681

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What are the two versions of Command Console Software?

Answer

We offers Standalone and Workgroup Editions of Command Console Software.

Answer Id: E14262

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Which protocol should I use to prepare my sample for hybridization to GeneChip Gene 1.0 ST Array and GeneChip Gene 2.0 ST Array?

Answer

The WT Plus kit or the WT Pico kit is recommended for preparing samples for use with the Gene 1.0 ST Array and the Gene 2.0 ST Array.

Answer Id: E14094

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

In the Command Console Software, what are data roots?

Answer

Data roots are Windows-based folders that store Command Console data. There is no limit to the number of data roots that users may define. Also, data roots can be defined on local, external or network drives. Command Console Software only recognizes files that are located within data roots.

Answer Id: E14234

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What are the basic quality assessment metrics for the GeneChip Exon Array?

Answer

The standard Affymetrix expression control sets (i.e., bacterial spikes) including both the hybridization control spikes and poly-A RNA control spikes are present on the Human Exon 1.0 ST Array and can be used to assess quality in a qualitative manner as used previously. As a new feature unique for the Exon Array, the Expression Console software supports the extraction of residuals from the PLIER model when running a multiple-array analysis. Such residuals can be used to identify outlier arrays and poor performing probes.

In addition, for most of the 100 normalization control genes used in the design of the GeneChip Human Genome U133 Array, probe sets representing both their intron and exon regions have been tiled on the Exon Array. The exon and intron probe set metrics (i.e., % detection p-value <= 0.05, mean/median signal) can be used as an additional method to identify problematic outlier arrays or analysis problems.

For these new experimental analysis metrics, there are no simple standard numeric threshold values that we can recommend at this moment as cutoffs for identifying good-performing or poor-performing arrays. However, it has been found that they are valuable when comparing relative values across a set of experiments for identifying outlier arrays. See the "Quality Assessment of Exon Arrays" (https://tools.thermofisher.com/content/sfs/brochures/exon_gene_arrays_qa_whitepaper.pdf) white paper for more information.

Answer Id: E13529

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

When I try to download library or annotation files for my array type in TAC, I do not find my array of interest listed as available for download. What should I do?

Answer

The list of array types for downloading library or annotation files in TAC covers the more commonly used array types. If you would like to analyze your expression data using our software, but your array is not on the list, please contact our technical support team for assistance. We can generate or provide the files necessary for analysis.

Answer Id: E14316

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

How many arrays are in the GeneChip Rat Expression Set 230?

Answer

Two arrays are in the set.

Answer Id: E13801

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

How do I analyze the data generated by the Axiom Genome-Wide BOS 1 Array Plate?

Answer

Axiom Analysis Suite is used to analyze data from the Axiom Genome-Wide BOS 1 Array Plate.

Answer Id: E14043

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What are the benefits of array registration?

Answer

Allows for filtering, sorting, and searching on user-defined attributes.
Allows users to define specific attributes associated with the physical arrays.
Allows managers to require the input of specific attributes to be associated with physical arrays.
Allows the saving of data to user-defined project folders as opposed to the system default folder.

Answer Id: E14251

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What is the recommended hybridization time for Thermo Fisher Scientific miRNA Arrays?

Answer

GeneChip miRNA Array 17 +/- 1 hr
Thermo Fisher Scientific miRNA Array Plates 17 +/- 1 hr
Thermo Fisher Scientific miRNA Array Strips 20 +/- 1 hr

Answer Id: E14138

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

The Expression Console Software displays an error when trying to download library files for the first time after installation of the software. What should I do?

Answer

a. Check Operating System of computer and make sure compatible with the Expression Console version installing.
b. Check to make sure the library path for Expression Console is local and not under “My Documents”. In Expression Console, Edit > Set library path
c. Uninstall Expression Console. Download the Expression Console package from our website. Unpackage the download. Right mouse click on the setup.exe file and “run as administrator”. Make sure the library path is local.

Answer Id: E14331

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What quality metrics can I examine to determine if dim or bright hybridizations have impacted my data?

Answer

Use either All_mean or PM mean to assay for hybridization intensity. All_mean is a probe-set metric. PM_mean is a probe-level metric, and is the mean of perfect match raw intensities prior to any transformations, such as normalization or probe summarization. PM_mean and All_mean can be compared to understand the effect that data processing steps have on the average intensity of an array because All_mean has been subject to any data transformations that have been performed during signal estimation and normalization. Apparent outliers only based on PM_mean can be ignored when corrected through data normalization in All_mean.

Answer Id: E14026

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Where can I find sample data for results from use of the Mouse Diversity Genotyping Array?

Answer

Please visit the website for sample data, including 98 classic mouse strains and 50 F1 crosses. The mouse breeds that the samples originated from have been anonymized since they are proprietary mouse strains.

Answer Id: E14161

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What procedure is used to generate the genome alignment data?

Answer

Genome alignments are currently provided for Human/Mouse/Rat/Drosophila/C elegans arrays. We align the target sequences against the genome sequence downloaded from the UCSC website using BLAT. While some of the target sequences do not align, perhaps due to the draft nature of several genomes, some targets align at multiple locations on the genome. We apply a filter to select the best hit for each target sequence.
We use the following procedure:

Calculate a score for each alignment as follows:

score=matches - (mismatches+5*qbaseinsert)
where matches = number of bases that match (including both repeat and non-repeat regions)
mismatches = number of bases that do not match in the alignment
qbaseinsert = number of bases inserted in the query

It is therefore possible that some of the scores are negative.

Pcgood=score*100/target size

The pcgood metric is provided on the website and in the download files.

Select the alignment with the best score.

Derive genomic coordinates for the probes (25-mers) from the "best" target sequence alignment.

We use the genomic coordinates for each probe (25-mer) from above and search for transcripts (RefSeq and GenBank mRNA alignments to the genome from UCSC genome database) that overlap with the alignment of the probes. In the NetAffx summary report, we provide the transcript whose genomic alignment overlaps with the maximum number of probes from that particular probe set. We also provide the total number of probes from the probe set that overlap with the transcript as measure of the ability of the probe set to detect the corresponding transcript.

Answer Id: E13479

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Where can I get a list of miRNAs represented on Affymetrix miRNA Array Plates?

Answer

You can get the list by downloading the annotation files that will be available on the website.

Answer Id: E14117

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

My genomic DNA sample for the Axiom array is showing RNA contamination, what can I do?

Answer

The biggest risk is underestimation of the amount of input gDNA. You should quantify by PicoGreen assay to ensure you are adding the correct amount of starting DNA into the reaction. The contaminating RNA should not affect the assay. If a PicoGreen assay is not an option, you may need to clean up the sample to get a better assessment of the actual amount and quality of gDNA.

Answer Id: E14287

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What other software components are installed with GTC 4.2?

Answer

The Microsoft .NET 2.0 framework, Java and Visual C++ runtime environments are installed with GTC 4.2.

Answer Id: E13672

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What are the array QC metrics for the CytoScan 750K Array?

Answer

The CytoScan 750K Array uses the following QC metrics:
SNPQC ≥15
MAPD ≤0.25
Waviness SD ≤0.12

These 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 which for which the majority of the genome is not mosaic. For hematological malignancy samples the baseline assumption pertaining to constitutional samples is violated with regard to of aberration frequency and high levels of mosaicsm 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 samples is a failure for that array result. There is no direct correlation between the passing numeric value for any one of the metrics and the quality of a sample. For example, a sample that has an SNPQC=30 is not necessarily a better quality sample than one that has an SNPQC=20.

Answer Id: E13932

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What is CytoScan Cytogenetics Suite?

Answer

CytoScan Cytogenetics Suite consists of CytoScan arrays and CytoScan Reagent Kit, GeneChip Command Console Software (AGCC), and Chromosome Analysis Suite (ChAS). It enables the performance of high-resolution, genome-wide DNA copy number analysis and also provides genotyping information for the detection of copy neutral loss/absence of heterozygosity (LOH/AOH), which can be used to detect uniparental isodisomy (UPD). The combination of high-resolution DNA copy number data and the ability to detect gains, losses, and UPDs on a single array makes CytoScan Cytogenetics Suite ideal for cytogenetics studies.

Answer Id: E13939

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Which files are required to use the Fluidics Station 450?

Answer

The fluidics scripts are required in order to run the Fluidics Station. Please see the demonstration in the training and tutorials (www.thermofisher.com/us/en/home/life-science/microarray-analysis/microarray-analysis-learning-center/microarray-analysis-training.html) section of the website for additional information.

Answer Id: E14245

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Can QC thresholds be modified in GTC 4.2?

Answer

Yes, QC thresholds can be modified in GTC 4.2. To modify the QC threshold options, click on the QC Thresholds shortcut on the main toolbar or select it from the Edit/QC Thresholds menu.

Answer Id: E13682

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

How much does it cost to use the NetAffx Analysis Center?

Answer

The NetAffx Analysis Center is available to both customers and non-customers at no cost. The only requirement for use is the completion of a short registration form (http://www.affymetrix.com/analysis/index.affx#1_1).

Answer Id: E13457

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What is the Command Console Standalone Edition?

Answer

The Standalone Edition is the desktop version of Command Console Software and is similar to GCOS workstation. Command Console Standalone has a web interface that provides sample registration, data organization, and administrative functionality. The standalone version is only accessible from the local computer and does not support remote connections. However, Command Console Standalone can use shared network storage to share data with other standalone workstations via the file system.

Answer Id: E14263

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

How much starting material is required for the Gene 1.0 ST and Gene 2.0 ST Arrays?

Answer

Using the Ambion WT Expression kit, a minimum of 50 ng of starting total RNA is required. No ribosomal RNA reduction of the starting material is required.

Answer Id: E14095

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

I added my exon library files to my library folder, but the application still will not analyze exon arrays. What should I do?

Answer

Examine the messages in the status window to identify the missing library files in Expression Console Software. If the computer is connected to the internet, use the download library files functionality to add the necessary files. In addition to these files, Expression Console Software requires two additional files for exon analysis: the qcc file ith control probe information and an exon_analysis_configuration file.

These files are automatically included when Expression Console Software is used to download the library files; however, if you manally add file to Expression Console Software, you will need to obtain the qcc and exon_analysis_configuration files from www.thermofisher.com.

Answer Id: E14015

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What data analysis software solutions are offered?

Answer

We provideTranscriptome Analysis Console Software for normalization, summarization,  differential expression analysis and visualization free of charge. Due to the presence of multiple organisms on the miRNA arrays, the chromosomal location feature in Transcriptome Analysis Console Software will not give accurate results.

For analysis in Transcriptome Analysis Console Software, array type-specific configuration and annotation files are required. Use the “Download Array Type Files” button in the Preferences tab to download and install array type-specific library files.

Answer Id: E14130

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Is the Clariom S capable of exon-level analysis?

Answer

No, the Clariom S array is not capable of exon-level analysis. The probes have selected to be the most constitutive probes, representing the most common areas of a gene model. This means that most of the exons in the gene model will likely not have representation on the array, meaning that it is not practical to enable exon-level analysis.

Answer Id: E14343

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Can I save query results for use at a later time when using the NetAffx Analysis Center?

Answer

Registered users of the NetAffx Analysis Center can save their work for later use. After you have logged into the site, all of your query results are saved in the Sessions page. Subsequent logins allow you to select the desired queries and click the "View" button to retrieve the corresponding entries. Query results can also be saved to your desktop by selecting the Results page and then clicking the "Save" button.

Answer Id: E13464

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What software is available for analysis for genoytping and copy number analysis?

Answer

All genotyping and copy number analysis is done with ChAS. CytoScan Cytogenetics Suite is not intended for genome-wide association studies.

Answer Id: E13995

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What is the typical yield range from PCR product purification?

Answer

The minimum recommended yield is 2.5 µg/µL for a sample. Yields can range from 3.0-4.5 µg/µL, and the average yield for seven or more samples processed in a run (not including the negative control) should be greater than 3.0 µg/µL. If the average yield is below this, consult the troubleshooting section of the CytoScan Assay User Manual (Cat. No. 703038, https://tools.thermofisher.com/content/sfs/manuals/cytoscan_assay_user_manual.pdf).

Answer Id: E13972

Was this answer helpful?

Yes
No
Thank you for your response