Search
Search
查看更多产品信息 GeneChip™ Human Genome U133A 2.0 Array - FAQs (900469, 900468, 900471)
17 个常见问题解答
The intended use of the 100 probe sets is to allow users to normalize data across the chip. These 100 probe sets are considered normalization controls. They were found to have consistent levels of expression across multiple tissue types and treatments.
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
Occasionally, it is not possible to select either a unique probe set or a probe set with all probes common among multiple transcripts ("_s_at" ). In such cases, similarity criteria are suspended, and the resulting probe set name is appended with the "_x_at" extension. These probe sets contain some probes that are identical, or highly similar, to unrelated sequences. These probes may cross-hybridize in an unpredictable manner with sequences other than the main target. Data generated from these probe sets should be interpreted with caution, due to the likelihood that some of the signal is from transcripts other than the one being intentionally measured.
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
The primary goal in probe set selection is to select a probe set unique to a single transcript or common among a small set of similar transcript variants. A probe set name is appended with the "_s_at" extension when all the probes exactly match multiple transcripts. The probe set selection process generally favors probe sets measuring fewer transcripts. Probe sets with common probes among multiple transcripts (the "_s_at" probe sets), are frequent and are to be expected, due to alternative polyadenylation and alternative splicing. In most cases, "_s_at" probe sets represent transcripts from the same gene, but the same probe set can sometimes also represent transcripts from homologous genes. One transcript may be represented by both a unique and an "_s_at" probe set when the transcript variation is sufficient.
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
There are two ways to export the CEL file from GCOS v1.4 as a text file.
1. In GCOS 1.4 use GCOS Manager to navigate to the CEL file in the process database. Highlight the CEL file and right click to export the data from the process tab. You may want to change the data location where the export will be stored before you start.
2. In GCOS 1.4 use the find feature in GCOS Manager to find the CEL files and export those selected as a text file. This approach allows export of more than one experiment at a time.
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
Command Console cannot generate a comparison analysis between different array types.
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
About 12 minutes per HG-U133 Plus 2.0 Array, comparable to scan time for a set of HG-U133A and HG-U133B Arrays.
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
About 7 minutes per array, comparable to the scan time of a HG-U133A Array.
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
About 70 MB.
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
About 175 MB.
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
Please contact Technical Support to obtain the high-resolution scanning patch.
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
Below is a list of circumstances and clarification regarding whether or not 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.
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 to GCOS analysis workstations.
d. GCOS Server upgrade: Your GCOS 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 HG-U133A 2.0 and HG-U133 Plus 2.0 Arrays. The HG-U133A 2.0 and HG-U133 Plus 2.0 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 when the high-resolution scanning patch has not been applied.
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
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.
For array hybridization, washing, staining and scanning, the following instrumentation is required:
-GeneChip Scanner 3000 7G
-GeneChip Fluidics Station 450
-GeneChip Hybridization Oven 640
Data acquisition and analysis of Human Genome U133 Plus 2.0 Arrays requires the following software:
-GeneChip Command Console Software
-Expression Console Software
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
Yes, the complete set of sequence information for the probes, target, and consensus/exemplar sequences represented on all catalog expression arrays, including the HG-U133 Set, is available. Please check the HG-U133 techncial note (https://tools.thermofisher.com/content/sfs/brochures/hgu133_design_technote.pdf).
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
The GeneChip Human Genome U133 Set incorporates significant advances in array design. The resulting two-array set is a powerful tool, providing you the best view of the human transcriptome.
Design features include:
-Using genomic sequences to verify sequence selection, orientation, and the quality of sequence clustering.
-Using clustering information from UniGene (Build 133), in combination with primary sequence and annotation information from a number of public databases, to give a more complete and accurate array design data set.
-Using probe selection methods that use a multiple linear regression model, derived from a thermodynamic model of nucleic acid duplex formation, which predicts probe binding affinity and linear signal response to varying target concentrations.
-Leveraging feature size reduction from 20 to 18 microns to allow for more probe sets per array, with no reduction in performance.
For more information on array design and probe selection of the HG-U133 Array, see the Array Design for the GeneChip Human Genome U133 Set Technical Note. (https://tools.thermofisher.com/content/sfs/brochures/hgu133_design_technote.pdf)
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
The probes on the HG-U133 Set are designed to detect the anti-sense strand of the gene of interest, and these probes are annotated with the "_at" extension. The primary goal in probe set selection is to select a probe set unique to a single transcript or common among transcripts from the same gene.
Often, it is not possible to select a probe set that is unique to a single transcript because multiple transcript variants share common sequence. Such probe sets are annotated with the "_s_at" extension. Occasionally, it is not possible to select a unique or shared probe set. Such probe sets are annotated with the "_x_at" extension. For more information, please review the _s_at and _x_at_ probe set descriptions.
Please note: There are no "_f_at", "_g_at", or "_r_at" probe sets in the HG-U133 design, as opposed to the HG-U95 Array design. This is because the nonunique probe set types were simplified and adjusted to account for improvements due to improved probe selection rules.
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.
The Human Genome U133 (HG-U133) Set, consisting of two GeneChip arrays, contains almost 45,000 probe sets representing more than 39,000 transcripts derived from approximately 33,000 well-substantiated human genes.
Find additional tips, troubleshooting help, and resources within our Microarray Analysis Support Center.