Documents & Support

MAPD 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.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Was this answer helpful?

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.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Was this answer helpful?

a. GeneChip Scanner 3000s that were shipped after September 15, 2003 with serial number 502xxx are enabled for high-resolution scanning.

b. GeneChip Scanner 3000s that were shipped prior to September 15, 2003 with serial number 501xxx that have had the GeneChip Scanner 3000 High-Resolution Update installed by an instrument service engineer are enabled for high-resolution scanning. A sticker is applied to the rear of the scanner to indicate that the upgrade has been performed.

c. Contact technical support at techsupport@thermofisher.com to inquire about a scanner upgrade.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Was this answer helpful?

The CytoScan Assay requires either the GeneChip Scanner 3000 7G System or the GeneChip Scanner 3000Dx v.2 with Data Transfer Server and a GeneChip Hybridization Oven 645.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Was this answer helpful?

a. GeneChip Scanner 3000s that were shipped after September 15, 2003 with serial number 502xxxxx are enabled for high-resolution scanning.

b. GeneChip Scanner 3000s that were shipped prior to September 15, 2003 with serial number 501xxxxx that have had the GeneChip Scanner 3000 High-Resolution Update installed by an instrument service engineer are enabled for high-resolution scanning. A sticker is applied to the rear of the scanner to indicate that the upgrade has been performed

c. Contact 888-DNA-CHIP or your local Affymetrix technical support to inquire about a scanner upgrade.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Was this answer helpful?

a. GeneChip Scanner 3000 that were shipped after September 15, 2003 with serial number 502xxxxx are enabled for high-resolution scanning.

b. GeneChip Scanner 3000 that were shipped prior to September 15, 2003 with serial number 501xxxxx that have had the GeneChip Scanner 3000 High-Resolution Update installed by an instrument service engineer are enabled for high-resolution scanning. A sticker is applied to the rear of the scanner to indicate that the upgrade has been performed.

c. Contact 888 DNA-CHIP or your local Affymetrix technical support to inquire about a scanner upgrade.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Was this answer helpful?

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

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Was this answer helpful?

The three lights (green, yellow, and blue) indicate the scanner's various states:
- Green OFF; Yellow OFF; Blue ON: Initial boot up
- Green ON; Yellow ON; Blue ON: Scanner boot up
- Green OFF; Yellow ON; Blue ON: Laser warm up
- Green OFF; Yellow Flashing; Blue ON: Scanner in error
- Green ON; Yellow OFF; Blue ON: System is ready
- Green Flashing; Yellow OFF; Blue ON: Scan in progress

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Was this answer helpful?

The use of the scanner requires a number of updated library files. Library files are installed in Command Console Software using the Library File Converter Tool. 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.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Was this answer helpful?

The GeneChip Fluidics Station 450 (FS450), GeneChip Scanner 3000 (GCS3000), and the GeneTitan Instrument.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Was this answer helpful?

Customers can run 48 samples per week (5 days) with three fluidics stations, 1 scanner, 1.5 technicians. Using the 96-sample protocol, customers can run 96 samples in 6 days, using the same instrumentation or 96 samples in 5 days using six fluidics stations and 2 scanners. If a group staggers the protocol during the week or has more instrumentation it is possible to get higher throughput, but this is the standard.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Was this answer helpful?

The CytoScan assay requires either GeneChip Scanner 3000 7G System with Workstation and AutoLoader or GeneChip System 3000Dx v.2 and a GeneChip Hybridization Oven 645.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Was this answer helpful?

-GeneChip Scanner 3000 7G System
-Fluidics Station 450 (Please note that the FS400 is not supported with SNP 6.0 arrays.)

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Was this answer helpful?

GCOS is the software that provides instrument control for the Fluidics Station 400 and GeneArray 2500 Scanner. GCOS, FS400, and GA2500 are discontinued products. For upgrade information, please contact your technical support team.

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Was this answer helpful?

Below are a list of circumstances and clarification on if the high-resolution scanning patch needs to be applied. Keep in mind that the high-resolution scanning patch must only be applied on top of GCOS, not AGCC software.

a. GeneChip Scanner 3000 (serial numbers 502xxxxx): The instrument service engineer has applied the high-resolution scanning patch to the computer that is controlling the GeneChip Scanner 3000 at installation, but not to the workstations or servers (see c and d below).

b. GeneChip Scanner 3000 (serial numbers 501xxxxx): The instrument service engineer will apply the high-resolution scanning patch to the computer that is controlling the GeneChip Scanner 3000 at the time of the upgrade, but not to the workstations or servers (see c and d below).

c. Analysis workstations and clients: You must apply the high-resolution scanning patch. d. Server upgrade: Your database administrator or an Affymetrix Software Support Engineer needs to apply the high-resolution scanning patch in coordination with the upgrade of server to GCOS.

e. Installation of library files post scanner installation or upgrade: The high-resolution scanning patch must be reapplied following the installation of library files for arrays that precede the Rat 230 2.0 Array. The Rat 230 2.0 array and library files are high-resolution-scanning ready. The error message "cannot read the parameters for probe array type from the database" appears when one tries to scan an array on a GeneChip Scanner 3000 high-resolution scanner but the high-resolution scanning patch has not been applied

Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.

Was this answer helpful?