If you have any technical questions regarding SpotReader, please look at our Frequently Asked Questions. If you still need answers, you may send an e-mail to our Support Team or call us at (415) 346-6461.
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Frequently Asked Question about SpotReader
Q. Every microarray gridding program says they have automatic gridding. What's so special about SpotReader?
SpotReader works! Try SpotReader, try the others. You'll see that we are not boasting idly. It's guaranteed.
Q. What do you mean by "guaranteed"?
If you're not satisfied with SpotReader, contact us within 30 days of your purchase and we will refund your payment. We don't claim 100% perfect grids on every scan, because background and printing problems can cause misalignment on a small percentage of images. But we've done extensive comparisons with other programs that claim automatic gridding, and SpotReader does a better job, especially on tough images. When problems do occur, fixing them is much easier with SpotReader's viewing and editing tools. Try it for yourself on your own images.
Q. Is SpotReader compatible with my scanner?
SpotReader can read any 16-bit TIFF file produced by any scanner. It does not control your scanner.
Q. On which computers does SpotReader run?
Windows NT, 2000, XP, ME, 98 with at least 128 megabytes of RAM and a hard drive large enough to hold your microarray images (about 20 megabytes each). It hurts to say so, but SpotReader does not run on Macintosh.
Q. Will my contact and payment information be kept private?
Yes. We will not distribute, rent, or sell your information to third parties, whether you are purchasing the program or just testing it. Your e-mail address is required to deliver the key that unlocks SpotReader after installation. We will send e-mail to you when new versions of SpotReader are available; you may request to be removed from this notification list at any time.
All personal information is transferred using a connection secured with 128-bit encryption.
This website uses cookies to identify registered users of SpotReader by means of a unique identification code. These cookies do not contain any personal information. This website tracks the browser type and IP address of all visitors for statistical purposes.
Q. Does SpotReader understand multi-image TIFF files?
Yes. SpotReader recognizes the format of the image file(s) you use, whether one multi-image file or two to four single-wavelength files. You don't need to specify the format.
Q. Can SpotReader handle four-color experiments?
Yes. SpotReader finds up to four companion files that are named according to the terms shown in the File/Folder Associations dialog (under the File menu). You can enter your own terms if the ones you use are not already listed. The Feature Information Toolbar automatically adjusts to show the four channels. You don't need to change any program settings when you switch between two- and four-color experiments.
Q. I need to export my data into a database. Will SpotReader results be recognized?
Some centralized database facilities have added SpotReader's .srr format to the list of accepted formats. If yours hasn't, SpotReader can write results to a GenePix® 5 format .gpr file. If your database or analysis progam can import such a file, it can import SpotReader's results. You can also open a results file (either .gpr or .srr) as a tab-delimited table in a program like Excel for other kinds of data analysis.
Q. Does SpotReader work on every kind of printed array?
Probably. It works on a rectangular-grid of one or more blocks, each block consisting of spots printed in either a rectangular grid or an "orange-packed" grid. All blocks must have the same number of rows and the same number of columns (even if some spot locations are empty). Each block can have up to 300 rows and 300 columns. At this time, SpotReader draws only elliptical or circular features, not rectangular ones. If you find SpotReader doesn't work for your type of arrays, please let us know.
Q. Sometimes spots are offset from the regular rows because of printing problems. Can SpotReader handle such patterns?
This can happen when printer has to be stopped and restarted during manufacture of the slides – not an unusual occurrence. After this kind of interruption, the printer often places subsequent features slightly out of alignment from those printed before the interruption. SpotReader offers two kinds of solutions for this kind of pattern. Jog Hints can be used to tell SpotReader where and to what magnitude a jump occurs in the pattern. This helps the program adjust spot locations automatically. When a Jog Hint is entered as part of a parameter set, all the slides in an affected print run can be auto-gridded successfully. A second tool is Pin Mode, in which features in a section of a block can be moved. Pin down certain features, and adjust others around the pins. These two powerful tools make it possible to get good data easily and effectively, even from irregular print runs.
Q. How do I change the automatic flagging settings?
When you are looking at an image, place the cursor over the tab (on the left side of the main window) marked "Flagging Parameters." The toolbar will pop out. Turn flag choices on and off with the check boxes, and change thresholds with the up- and down-arrows. Flags are instantly updated on the image, so you can see exactly which features are flagged or un-flagged as you change parameters. If a spot is flagged, the reason is shown on the Feature Information Toolbar in a one-letter code. Hold down the Ctrl key and place the cursor over the code to bring up a translation.
Q. What's the best way to figure out all the keyboard shortcuts?
Click on Array | Common Keyboard Shortcuts or Advanced Keyboard Shortcuts. Navigation shortcuts are listed in both since they are frequently used. Other shortcuts are shown in this menu so they are always available; you don't have to open the Help to find a shortcut.
Q. Can I inspect an image and grid while another one is being processed?
Yes. If you drag and drop several image files into the database, they will be processed (gridded) in the background as soon as parameters are available. You can view images before, during or after a grid is made. Processing (gridding and flagging) is fairly memory-intensive, so depending on your computer the program may be sluggish when images are processing in the background. Your presence is not required for gridding, so you can let the computer do it while you spend your time on something else, and come back to inspect the grids when it's finished.
Q. How can I learn more about SpotReader's features?
First, take the Video Tours (click on the link on the sidebar of this page). When you run the program, the Help files give step-by-step directions for using SpotReader's unique features such as File/Folder associations, batch processing, automatic flagging (including computations), customizing the results table, and so on. Click on Help | Help Topics. Or use context-sensitive help - pressing F1 brings up help for dialog boxes, windows, toolbars, and so on. Or click on the "what's this?" icon (an arrow with a question mark over it), and then click on the window or icon for which you want help.
GenePix is a registered trade mark of Axon Instruments.
