Resource 149640

Name: Probeset usage

Various filters were applied to the raw genotyping results to derive a unique set of high-reliability Calls. This file summarises, on a batch-by-batch basis, the results of the checking operations used to produce the final distributed values. In addition, some loci were tested using multiple probesets and it was necesary to identify which (if any) probeset gave the best result on any particular batch.

The columns in the file are as follows:

  1. Batch ID;
  2. Affymetrix SNP ID;
  3. Affymetric probset ID;
  4. Test: locus sufficiently well-defined in annotation dictionary;
  5. Test: locus present on the array used to genotype current batch;
  6. Test: probeset regarded as performing well by Affymetrix;
  7. Test: probeset judged to be the best available (when more than one used for a SNP), or only one;
  8. Test: WTCHG quality-control indicates final Calls are reliable.
A value of 'x' in a column indicates that the corresponding test meant that results from that probeset could not be used in the particular batch. Note that probesets which failed one test were not necessarily tested with the others, so a 'u' by itself does not mean that a particular test was applied and passed.

To appear in the final Calls results, a locus/probeset combination must pass all 5 tests and would have 5 'u' values listed alongside it. These rows (around 85% of combinations) have been removed from the file to save space.

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