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Microarray interconversion software tools | Microarray data analysis

Robust conversion between microarray platforms is needed to leverage the wide variety of microarray expression studies that have been conducted to date. Currently available conversion methods rely on manufacturer annotations, which are often incomplete, or on direct alignment of probes from different platforms, which often fail to yield acceptable gene-wise correlation.

Source text:
(Brown and Patel, 2015) aRrayLasso: a network-based approach to microarray interconversion. Bioinformatics.

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DAVID / Database for Annotation, Visualization and Integrated Discovery
Allows users to obtain biological features/meaning associated with large gene or protein lists. DAVID can determine gene-gene similarity, based on the assumption that genes sharing global functional annotation profiles are functionally related to each other. It groups related genes or terms into functional groups employing the similarity distances measure. This tool takes into account the redundant and network nature of biological annotation contents.
aRrayLasso
Uses the Lasso-penalized generalized linear model to model the relationships between individual probes in different probe sets. We have implemented aRrayLasso in a set of five open-source R functions that allow the user to acquire data from public sources such as GEO, train a set of Lasso models on that data, and directly map one microarray platform to another. aRrayLasso significantly predicts expression levels with similar fidelity to technical replicates of the same RNA pool, demonstrating its utility in the integration of data sets from different platforms.
AbsIDconvert
A methodology for converting between genomic identifiers by first mapping them onto a common universal coordinate system using an interval tree which is subsequently queried for overlapping identifiers. AbsIDconvert has many potential uses, including gene identifier conversion, identification of features within a genomic region, and cross-species comparisons. The flexibility of this tool allows for custom definition identifier domains contingent upon the availability and determination of a genomic mapping interval.
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