TIGR Spotfinder Exercise (Tue Nov 21 2006)
   ==========================================
   Follow-up course of Microarray Data Analysis
   Nov 20-24 2006, PICB Shanghai
   Peter Serocka

1. Load a pair of scanned slides from /picb/course/10-Manila-Slides

2. Help: Open the Help window from Spotfinder's menu bar and locate
   the "Procedure description". What information is needed to compose
   a Grid? (Hint: step 3 in the Procedure description).

3. Grid Construction: In the Analysis Window, measure the required
   values for creating a grid, use the X:Y position display at bottom.
   Create a grid of one row, containing four blocks.

4. Align Grid blockwise to the top row of the slides. 
   Switch on "Contour" (left) and process each block. Is the color scheme
   used for the contours useful?

5. Quality visualistion: Switch to QCview, try out view A and view B.
   How is the color scheme related to contour colors in Analysis view?

6. In Analysis view, improve the block alignments to get a larger number
   of good spots. Observe the effect of background cutoff, found in "Gridding
   and Processing" (left). Save the grid to a file in your home directory.

7. Switch to Data view and inspect some spots, by clicking on their data
   rows. What can you see from the Background/Spot histograms? Get help
   by right-clicking the mouse on a histogram ("What's this" -> "More...".
   Note: Such context help also work in other parts of Spotfinder!)
 
8. While in Data view, switch to "Post Processing" (left). When do changes
   to the QF filter show up in the data view?

9. While in Data view, switch to "Cell Editor" (left). When do changes
   to the QC filter show up in the data view? Can you optimize the
   QC of a spot by adjusting its cell position and size?

10. Switch to RIplot and search for outliers. Clicking on a data point
    with bring you to Data view and the Cell Editor. Fix an outlier
    or "flag" is as bad.

11. Switch back to RIplot and "Post Processing" (left). What is the effect of
    QC threshold settings to the RI plot?

12. Annotation. Create a copy of /picb/course/20-Operon-Slides/OPHSV4.GAL
    in your home directory and rename it as OPHSV4.gal . Using TextEdit,
    change "ID" to "UID" in the header line (just after the "Block" lines).
    In Spotfinder, load this file as annotation (menu bar: Data menu)
    and from the same menu, "Set UID from annotation". 

13. Save data. In Data view, check the "Annotation" and the "MEV data"
    tabs. Do the annotation names show up as UIDs in the MEV data?
    Save the data as MEV file to your home directory