What are Best Probes? |
Some probe filters and probe design methodologies select the "best" probes from a given set of probes. To do this, eArray typically groups probes based on their primary accession, and selects the best probes among those with the same primary accession. When you define probe filter criteria, you can group probes in other ways as well, such as by Probe IDs, Gene Symbols, or Gene Names.
The metrics for selecting the best probes are:
Is the probe validated? (A validated probe is better than a non-validated probe.)
How close is the probe to the 3’ end of the primary accession? (Closer is better.)
When it defines the best probes, eArray first searches for validated probes within a primary accession, and then searches the validated probes to find the probes closest to the 3’ end within that primary accession. If none of the probes within a primary accession are validated, then eArray directly searches for the probes closest to the 3’ end to determine the best probes.
Certain types of probes, such as certain CGH and ChIP probes, and all Agilent SNP probes, have a performance score that reflects the likelihood that the given probe will produce a good log ratio response when it is used on the Agilent microarray platform. You can design a custom filter to limit certain search results to only the best performing probes. Also, when you set up certain types of searches, such as SNP probe searches by genomic interval, you can limit the number of returned probes. eArray uses probe scores as a basis to select the best probes to return. See Set up a CGH/ChIP Probe Scoring job and Search for SNP probes.