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XPN specifications

Information


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

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  • person_outline Andrey Shabalin <>

Publication for cross-Platform Normalization

XPN in pipeline

2015
PMCID: 4924658
PMID: 26575329
DOI: 10.18632/oncotarget.5876

[…] various cross-study normalization algorithms such as empirical bayes (eb) [], median rank scores (mrs) or quantile discretization (qd) [], nordi [], quantile discretization normalization (qdisc) [], xpn [] and median rank score normalization (mnorm) [] were employed to decrease non-biological bias and variance. since eb method has been applied widely to a large variety of microarray datasets […]


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XPN in publications

 (15)
PMCID: 5884535
PMID: 29617451
DOI: 10.1371/journal.pone.0194844

[…] datasets and provide reliable integration, removing batch effects and making cross-platform corrections, such as distance weighted discrimination (dwd) [], empirical bayes methods (combat) [], and cross-platform normalization (xpn) []. in this sense, combat and xpn have been proven to outperform dwd in term of minimizing inter-platform variance []., in this study, an integrated meta-analysis […]

PMCID: 5928887
PMID: 29721077
DOI: 10.7150/thno.23877

[…] only when the specific release of the mirbase database used for platform design was reported. for these platforms, mirna name was used for annotation based on the corresponding mirbase release. cross-platform normalization was used to estimate and minimize the effects from dataset-specific noise. in this process, arrays are filtered to obtain expression data associated with the phenotype […]

PMCID: 5854290
PMID: 29556515
DOI: 10.18632/oncoscience.395

[…] database. data preprocessing and normalization steps were performed in r version 3.1.0 using deseq package from bioconductor. to adjust for the possible batch and processing effect we have employed xpn algorithm (r package, conor), as previously described []. the resulting matrix contained mrna expression information for over 20k genes across all analyzed samples. normalized gene expression […]

PMCID: 5821872
PMID: 29467463
DOI: 10.1038/s41467-017-02696-6

[…] data preprocessing and normalization steps were performed in r version 3.1.0 using deseq package from bioconductor. to adjust for the possible batch and processing effect, we have employed the xpn algorithm (r package, conor). the resulting matrix contained mrna expression information for over 20k genes across all analyzed samples. normalized gene expression data were loaded into ipanda,. […]

PMCID: 5626145
PMID: 28767591
DOI: 10.1097/MD.0000000000007673

[…] quartile normalization was performed using the preprocesscore[] in r, and the gene expression matrix of each sample was acquired., all expression estimates were log2 transformed and merged using cross-platform normalization, which was performed using the conor[,] package in r. if different studies comprised similar or common gene symbols, 2 expression data of the same gene symbols […]


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XPN 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
XPN 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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