frmaTools

"frmaTools" is an R package designed to extend the usability and applicability of the Frozen Robust Multi-array Analysis (fRMA) preprocessing algorithm for microarray data. fRMA represents a significant advancement in microarray preprocessing, enabling the analysis of arrays individually while maintaining the benefits traditionally associated with multi-array methods. "frmaTools" achieves this through frozen parameter estimates derived from a comprehensive database of publicly available arrays. However, generating these estimates is resource-intensive, limiting fRMA's implementation to the most commonly used Affymetrix platforms.

frmaTools addresses this limitation by allowing users to create their frozen parameter vectors, thus enabling the customization of fRMA to a broader range of microarray platforms and specific research needs. The package simplifies curating a database and generating frozen parameter estimates, seamlessly integrating into the microarray preprocessing workflow. Moreover, frmaTools explores the necessary size of the training dataset for generating reliable estimates and discusses scenarios where creating a custom fRMA implementation might be particularly beneficial.