You searched for: 

genechip products

Product FAQ

Where can I download the HapMap CEL files for SNP 6.0 array?

Answer

The SNP 6.0 HapMap CEL files have been archived by NCBI. The files are available for download through the NCBI ftp server. To get the full set of CEL files, all the files with the extension .tgz should be downloaded. Any .tgz files will need to be extracted (or unzipped) twice. There is freeware called 7-Zip File Manager that can be used to extract the files. For additional information, please contact support.

Answer Id: E14295

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What is the hybridization temperature and rotation speed for CytoScan arrays?

Answer

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

Answer Id: E16629

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What format is the GeneChip Gene 1.0 ST Array?

Answer

The GeneChip Gene 1.0 ST Array is an 81/4 format. Please note that 81/4 format is to be treated equivalent to 100 format arrays.

Answer Id: E14099

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

What are the definitions of the array QC metrics terms "MAPD" and "SNPQC"; what does each metric measure and how are they used in assessing array performance?

Answer

MAPD: Median of the Absolute values of all Pairwise Differences is a per-microarray estimate of variability, like standard deviation (SD) or interquartile range (IQR). It measures the variability in log2 ratios by looking at the pair difference of all probes and taking a median value. The effect of an occasional big difference in log2 ratios between probes is removed by taking a median value and not a mean. This variability can come from different sources: Intrinsic variability in the starting material, hybridization cocktail preparation, microarray, or scanner.

Apparent variability induced by the fact that the reference may have systematic differences from the sample on this microarray. Regardless of the source of variability, increased variability decreases the quality of the CN calls. A high MAPD can be attributed to any of the above factors and indicates that CN calls may be inaccurate, leading to a higher false positive/negative rate.

SNPQC: This is a measure of how well genotype alleles are resolved in the microarray data. In other words, it estimates the distributions of homozygous AA, heterozygous AB, and homozygous BB alleles and calculates the distance between them. The better the separation of these distributions, the better the ability to identify a genotype based on its cluster position. The larger the difference between the peaks and the troughs, the better the resolution of homozygotes and heterozygotes and the higher the SNPQC metric is. If the three peaks are not well resolved, the difference between peaks and troughs will be low, resulting in a lower SNPQC value. A low SNPQC value indicates that quality of the SNP allele data is compromised, due to higher noise within the array, which compromises the overall quality and clarity of results.

Answer Id: E13996

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Can I use the WT Sense Target Labeling Assay protocol for prokaryotic arrays?

Answer

This has not been tested at the moment; therefore, it is not recommended to use the protocol for any application other than on the Exon Arrays.

Answer Id: E13655

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

I cannot see gene descriptions when I analyze the .dat file in Microarray Suite 4.x. How do I fix this?

Answer

First, verify that you are running the correct version of the Library Files (starting with November 2000), and that you are running Microarray Suite version 4.0.1 (required). If these versions are correct and you still encounter the problem, then there is, most likely, something wrong with the Microsoft Data Engine (SQL Manager). Contact us by e-mail at techsupport@thermofisher.com.

Answer Id: E13617

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

Can I track the samples that I have uploaded in the database?

Answer

If an xxCHP file has been previously published to the database, you will receive a warning indicating this sample already exists in the database. You can choose to overwrite the existing information or cancel to keep the existing information. It is important to back up and archive the ARR, CEL, CYCHP, and CHPCAR files at a minimum. This will allow you to maintain the ability to either reanalyze from the CEL file or revisualize the results using the CYCHP/CHPCAR files.

Answer Id: E13886

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

How do I see the Gene Names for the probe set IDs?

Answer

To see the NetAffx information associated with a particular probe set, view the probe level summaries under the REPORT menu item and double click on the probe ID of interest.

Answer Id: E14012

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

Once I have deleted a file from the ChAS database, is there a way to recover the file?

Answer

No, once a file has been deleted, the only way to replace that file in the database is to publish the original xxchp file again.

Answer Id: E13895

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

How were the normalization controls determined in the GeneChip Mouse Expression Set 430?

Answer

A candidate list of probe sets was obtained in collaboration with an external site based on a large number of tissue samples run on MG-U74v2 arrays. Criteria for selection included evidence of constitutive expression (detection in at least 95% of replicates) and minimal variation in signal across the tissues tested. The 11 probe pair probe sets for these transcripts were evaluated by hybridizing 11 tissues and 4 cell lines on Mouse 430A and B arrays. One hundred probe sets were selected that had detection in at least 95% of replicates and had minimal signal variation. Preference was given to RefSeq sequences where possible, probe sets were selected to give a range of signal values and to represent 100 unique UniGene clusters.

Answer Id: E13730

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

How do you move the .cel files out of GCOS to be imported into Expression Console?

Answer

GCOS users must use DTT v1.1, using the Flat File option, to transfer files to be analyzed by the Expression Console software from the GCOS database to an independent folder.

Answer Id: E13538

Was this answer helpful?

Yes
No
Thank you for your response

Product FAQ

What are the general genomic DNA requirements for the CytoScan assay?

Answer

DNA must be double-stranded genomic DNA.
DNA must be free of PCR inhibitors.
DNA must not be contaminated with other human genomic DNA sources or with genomic DNA from other organisms.
DNA must not be degraded.
DNA should have an A260/A280 between 1.7-2.1 (numeric rounding allowed).

Answer Id: E13949

Was this answer helpful?

Yes
No
Thank you for your response