Test procedures for merged data

One of the new features of BASE 2 is that it keeps track of all links back to the raw data for each spot in a bioassayset. In BASE 1 this the link was limited to one raw data for each spot. When doing a merge of spots having, for example, the same reporter it was impossible to keep the link to all raw data that spot was calculated from. You could choose to link to one of the spots or to none at all. With BASE 2 it is possible to keep all the links but it creates some other problems which must be solved:

It is actually more or less the same problem. How do we select a raw data value when there is many to choose from? Should we always average or do we need other options (max, min, sum, count, etc)?

Contents
  1. Summary of the test procedure
See also
  1. Ticket #215: Incorrect use of DynamicSpotQuery in table view, plot function, filter function, etc.

Last updated: $Date: 2008-09-05 17:15:25 +0200 (Fri, 05 Sep 2008) $

1. Summary of the test procedure

This test procedure sets up an experiment with some merged data. After that it is expected that the web interface is used for trying out various ideas and testing that the desired functionality is working correctly.

  1. We recommend starting with a fresh installation, though it is relly neccesary.
  2. The test is running as the root user which must have the password "root".
  3. 10 reporters are created (if they don't exists): MERGE:0, ... MERGE:9
  4. An array design is created with 55 features in ten blocks. The first block has one spot of each reporter, the second block reporters 1 to 9, and so on until the last block which only has reporter 9.
  5. Two raw bioassays are created and raw data is generated. We only generate data for the mean foreground intensities. The reporter number modulo 3 is used to up- or downregulate each spot. 0, 3, 6, and 9 are downregulated, 2, 5, and 8 are upregulated. A random noise term is also added.
  6. An experiment is created and a root bioassayset is created from the mean foreground intensities.
  7. Two child bioassaysets are created. One which merge the two bioassays together to one bioassay by taking the mean of the spot intensities for each position. The second bioassayset merges reporters for each bioassay.

This test doesn't need any data files.

To run the test do the following:

  1. Compile the core and the test programs: ant main test.
  2. Change to the build/test/ directory.
  3. Run test programs: ./test.sh merge <cmds> where <cmds> is one or more of the following: More tests may be added in the future.