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CONOR specifications

Information


Unique identifier OMICS_14604
Name CONOR
Alternative name CrOss-platform NOrmalization in R
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.0.2
Stability No
Requirements
CLSOCP, tseries, outliers, nortest, quadprog, zoo, preprocessCore, fields, fpc, flexclust, plyr
Maintained No

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Publication for CrOss-platform NOrmalization in R

CONOR in pipeline

2014
PMCID: 4168973
PMID: 25233347
DOI: 10.1371/journal.pcbi.1003851

[…] probe intensities as the gene expression. all the data sets were normalized independently between array using limma package . to minimize batch effects across different data sets, we used the conor package with the bayesian method ., we generated the pam50 heatmap of the gene expression data and the correlation heatmap with hierarchical clustering, where euclidean distance measure […]


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CONOR in publications

 (7)
PMCID: 5928887
PMID: 29721077
DOI: 10.7150/thno.23877

[…] to retain only the mirna that are represented on all array platforms. array-filtered, transformed and mirna-filtered data is normalized across platforms using the xpn algorithm implemented with the conor package in the r statistical environment. data summarization plots, including boxplots, two-dimensional pca projections, and hierarchical clustering were used for quality control […]

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

[…] 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 were normalized for producing a new dataset. then, the newly produced […]

PMCID: 4227423
PMID: 25242495
DOI: 10.3892/mmr.2014.2585

[…] data (). thus, cross-platform normalization (xpn) was used (). we selected the 12,779 common genes between the two datasets and their expression data were normalized with the xpn method using the conor package (). these data were used for further analyses. the degs were identified from the normalized final dataset using student’s t-tests (p<0.05), followed by benjamini-hochberg (bh) […]

PMCID: 4168973
PMID: 25233347
DOI: 10.1371/journal.pcbi.1003851

[…] probe intensities as the gene expression. all the data sets were normalized independently between array using limma package . to minimize batch effects across different data sets, we used the conor package with the bayesian method ., we generated the pam50 heatmap of the gene expression data and the correlation heatmap with hierarchical clustering, where euclidean distance measure […]

PMCID: 4106758
PMID: 25051057
DOI: 10.1371/journal.pone.0100576

[…] (http://rmaexpress.bmbolstad.com/) prior to merging each other. we selected genes from all platforms based on the nih entrez gene id and used the median rank score method with the r package conor for cross-platform normalization (). the detailed procedure for performing the meta-analysis was provided in the supporting information (). in the analysis of bioconductor limma package […]


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CONOR institution(s)
Biomedical Informatics Research Center, San Diego State University, San Diego, CA, USA
CONOR funding source(s)
This work was supported in part by the National Institute of Health (NIH) Grant U54-HL108460.

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