| 1/3 | id: | 8 | | protocol_name: | Affymetrix MAS 5.0 Standard Scanning at NASC | | scanner_type: | | | scanning_software: | MAS5.0 | | description: | Scanning Protocol Information
Name: Affymetrix MAS 5.0 Standard Scanning
Width of Image Produced (Pixels): 4733
Height of Image Produced (Pixels): 4733
X Resolution (microns): 3
Y Resolution (microns): 3
Scanner Name: Agilent 2500A GeneArray Scanner
Software Name: Affymetrix Micro Array Suite 5.0
Image Analysis Information
Name: Affymetrix MAS 5.0 Standard Image Analysis
Software Name: Affymetrix Microarray Analysis Suite 5.0
Normalisation Information
Strategy Name: Affymetrix MAS 5.0 Scaling Protocol
Algorithm: The top 2% and bottom 2% of signal intensities are excluded, then the mean is calculated. The original signal values are scaled such that the mean is made equal to 100.
Control Elements:
none
| | remark: | Used at Nottingham Arabidopsis Stock Centre's (NASC) Affymetrix service. | | last_update: | 2004-02-24 19:47:26 | | login_id: | da_xia | | resource: | Affymetrix manual |
| 2/3 | id: | 4 | | protocol_name: | Affy- Array Scanning | | scanner_type: | GeneChip® Scanner 3000 | | scanning_software: | MAS5.0 | | description: | CHAPTER 4 Eukaryotic Arrays: Scanning 2.4.19
Eukaryotic
1. Select Run °˜ Scanner from the menu bar. Alternatively, click the Start Scan icon in
the tool bar. The Scanner dialog box appears with a drop-down list of experiments that have not been run.
2. Select the experiment name that corresponds to the probe array to be scanned.
A previously run experiment can also be selected by using the Include Scanned
Experiments option box. After selecting this option, previously scanned experiments
appear in the drop-down list.
3. By default, for the GeneArray® Scanner only, after selecting the experiment the number [2] is displayed in the Number of Scans box to perform the recommended 2X image scan. For the GeneChip® Scanner 3000, only one scan is required.
4. Once the experiment has been selected, click the Start button.
ÅÀ A dialog box prompts you to load an array into the scanner.
5. If you are using the GeneArray® Scanner, click the Options button to check for the
correct pixel value and wavelength of the laser beam. If you are using the GeneChip Scanner 3000, pixel resolution and wavelength are preset and cannot be changed.
6. Open the sample door on the scanner and insert the probe array into the holder. Do not force the probe array into the holder. Close the sample door of the scanner.
7. Click OK in the Start Scanner dialog box.
The scanner begins scanning the probe array and acquiring data. When Scan in
Progress is selected from the View menu, the probe array image appears on the
screen as the scan progresses. | | remark: | | | last_update: | 2003-09-05 09:39:30 | | login_id: | caldo | | resource: | Affymetrix manual |
| 3/3 | id: | 9 | | protocol_name: | GenePix Pro Scanning | | scanner_type: | | | scanning_software: | other | | description: | Scan at PMT 600, 500 | | remark: | | | last_update: | 2005-10-20 14:23:53 | | login_id: | HakeOligo | | resource: | |
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