This is a user manual for Agilent CGH eArray custom CGH microarrays
This document serves as a Frequently Asked Questions (FAQ) guide for users of the Agilent eArray software, specifically focusing on the design of custom Comparative Genomic Hybridization (CGH) microarrays. It details the process of creating probe groups, including methods such as searching the Agilent HD-CGH database, uploading custom probes, and using genomic tiling.
The text provides technical guidance on determining the appropriate number of probes and probe density for a given genomic region, explaining the impact of probe spacing on hybridization and data noise. It also compares the performance of probes generated via the 'Genomic Tiling' function against those selected from the Agilent HD-CGH Probe Database, recommending the latter for optimal results.
A Probe Group consists of one or more probes assigned to a group, and content is added by associating it with one or more Probe Groups.
The minimum number depends on the size of the aberration and the number of probes preferred to make an aberration call, while the maximum is limited by hybridization noise.
It is a value between 0 and 1 that predicts the likelihood a probe will produce a good log ratio response based on sequence parameters.