What is ArrayInitiative?

ArrayInitiative is a standalone, cross-platform, rich client desktop application for creating custom versions of a manafactuer-provided (default) microarray specification files.

Why is ArrayInitiative unique?

Several groups have published methodologies for re-defining probe sets, and, in some cases, have produced publicly available custom CDFs that reflect these changes. So why develop ArrayInitiative? The publicly available custom CDFs are tightly integrated with a particular probe set re-definition methodology. While each has significant strengths for specific biological questions, a more flexible approach is needed. Such an approach will allow other, novel probe set re-definition strategies -- or novel combinations of existing ones -- to be implemented, according to the experimental needs and characteristics of the samples. We designed ArrayInitiative to be a methodology-agnostic tool, available to any lab, for creating custom CDFs that conform to a custom re-definition methodology in order to answer study-specific biologic questions.

How is ArrayInitiative useful?

Since ArrayInitiative is not tied to a specific methodology for re-defining probe sets, it enables researchers to create new and unique CDFs based upon their own requirements. These CDFs might be the result of a new probe-filtering technique or may help to answer a specific biological question. Since it is unclear which probe set definitions -- current or future -- are the best, another advantage of ArrayInitiative is that it makes it easier to test alternative, competing definitions against standard Affymetrix-provided CDFs.

Software features

  • Import default array specifications (e.g. Affymetrix CDF).
  • Import probe sequences for the default array specification. For Affymetrix CDFs, the mismatch probe sequences are automatically generated.
  • Define and import a custom array specification, using a simplified specification format (delimited or XML).
  • Export any array specification to its standard format (e.g. CDF) or to several simple, non-standard formats.
  • Export any array specification to its standard format (e.g. CDF) or to several simple, non-standard formats.
  • Export the probe sequences for any array specification
  • Browse high-level information about an array, such as version and number of probes.