sva pipeline

sva specifications

Information


Unique identifier OMICS_00861
Name sva
Alternative names Surrogate Variable Analysis, fSVA
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 3.24.4
Stability Stable
Requirements mgcv, genefilter, BiocParallel
Maintained Yes

Subtools


  • fSVA
  • qSVA

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Documentation


Maintainers


  • person_outline Jeffrey Leek <>
  • person_outline John D. Storey <>
  • person_outline W. Evan Johnson <>
  • person_outline Andrew E. Jaffe <>

Publications for Surrogate Variable Analysis

sva IN pipelines

 (6)
2017
PMCID: 5550424
PMID: 28794406
DOI: 10.1038/s41467-017-00212-4

[…] blood and aml samples, a batch correction between aml and healthy cells was performed on quantile-normalized log2-values, using the parametric combat algorithm as implemented in the r package sva50., the performance of unsupervised (class discovery) algorithms depends on the number of features used as input. to reduce the noise inherent to any high-dimensional data set, selection […]

2017
PMCID: 5617529
PMID: 28977969
DOI: 10.18632/oncotarget.19315

[…] different series were merged together according to the gene symbol and any genes missing in any series were excluded. the batch adjustment between different geo series was completed using package sva in r software [30]. combat function was effective to adjust for known batches using an empirical bayesian framework [31]., in order to confirm the effects of batch adjustment and also […]

2016
PMCID: 4905462
PMID: 26848979
DOI: 10.18632/oncotarget.7152

[…] the samples were analyzed in three different batches consisting of two bead chips in each batch. to adjust for batch effects we used the combat implementation in the r/bioconductor package sva [28]. the chip number was used as batch covariate, and the tissue type was used as the sole biological covariate. the samples clustered according to tissue type and not chip or array […]

2016
PMCID: 5091760
PMID: 27806114
DOI: 10.1371/journal.pone.0166090

[…] of the affy bioconductor package [42] with geneannot based custom cdf (gahgu133plus2 v2.2.1) [43]. the log-2 normalized intensities were adjusted for batch effects by using combat function of the sva bioconductor package [44]. the cmdscale function was used for multidimensional scaling (mds) analysis before and after batch correction. the analyses were performed within the r environment. two […]

2012
PMCID: 3351145
PMID: 22262733
DOI: 10.1093/nar/gkr1265

[…] power or false positives. in a microarray meta-analysis, these systematic variabilities should be considered and incorporated in the analysis whenever possible. leek and storey (138) proposed surrogate variable analysis (sva) to further account for unmeasured and unmodeled factors in a genome-wide expression analysis. the result has shown improved sensitivity and accuracy. similar […]

sva institution(s)
Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA; Center for Bioinformatics and Computational Biology, Department of Computer Science, University of Maryland, College Park, MD, USA
sva funding source(s)
Supported by NIH (R01GM105705 and R01GM103552) and by a Bloomberg Fellowship.

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