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XPN | Merging two gene-expression studies via cross-platform normalization

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Allows to merge two gene expression studies. XPN is a block model-based method that has three parameters: the number of row and column clusters (K and L) and the number of basic iterations B. In principle, the XPN method procedure can be used with any clustering method that produces a pre-specified number of clusters from a given set of vectors, or with resampling, based improvements of such methods. The software was applied the three datasets without incurring substantial overfitting.

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XPN classification

XPN specifications

Unique identifier:
OMICS_00863
Software type:
Application/Script, Package/Module
Restrictions to use:
None
Output data:
The average of the normalized values obtained over the repeated runs.
Programming languages:
MATLAB
Stability:
Stable
Name:
cross-Platform Normalization
Interface:
Command line interface
Input data:
The gene-expression measurements from two studies, after appropriate preprocessing and imputation.
Operating system:
Unix/Linux, Mac OS, Windows
Computer skills:
Advanced
Maintained:
Yes

XPN distribution

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XPN support

Maintainer

  • Andrey Shabalin <>

Credits

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Publications

Institution(s)

Department of Statistics and Operations Research, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Mathematical Sciences, Norwegian University of Science and Technology, Trondheim, Norway; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, NC, USA; Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina, Chapel Hill, NC, USA

Funding source(s)

Supported by National Science Foundation Grant (DMS 0406361), National Cancer Institute Breast SPORE program to University of North Carolina at Chapel Hill (P50-CA58223-09A1), National Cancer Institute (RO1- CA-101227-01) and the Breast Cancer Research Foundation.

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