Microarray track

This document attempts to explain the microarray tracks on the browser in pretty extensive detail. The gene sorter has a somewhat different strategy for microarrays.

Database Representation

At the most basic level, the data for set of microarrays is stored in two tables:

1. A bed 15 table, containing both the probe information and the experimental data. The first 12 fields of this table are normal bed fields (excluding the bin field). These mainly describe the positioning of a gene or whatever item. Fields 10-12 deal with exons. Microarray tracks may have exons, but usually the convention is to set the blockCount=1, blockStarts=0, and blockSize=chromEnd-chromStart... i.e pretending there's only one exon.
   1. chrom
   2. chromStart
   3. chromEnd
   4. name
   5. score
   6. strand
   7. reserved/itemRGB
   8. thickStart
   9. thickEnd
   10. blockCount
   11. blockSizes
   12. blockStarts
   13. expCount
   14. expIds
   15. expScores
2. An expRecord table containing details concerning each of the experiments outlined in the bed 15 table.

Microarray Custom Tracks

The microarray custom track format is similar to a normal BED custom track format with the addition of some parameters to the "track" header.