sva

Package: sva
Title: Surrogate Variable Analysis
Version: 3.20.0
Author: Jeffrey T. Leek <jtleek@gmail.com>, W. Evan Johnson <wej@bu.edu>,
Hilary S. Parker <hiparker@jhsph.edu>, Elana J. Fertig <ejfertig@jhmi.edu>,
Andrew E. Jaffe <ajaffe@jhsph.edu>, John D. Storey <jstorey@princeton.edu>
Description: The sva package contains functions for removing batch
effects and other unwanted variation in high-throughput
experiment. Specifically, the sva package contains functions
for the identifying and building surrogate variables for
high-dimensional data sets. Surrogate variables are covariates
constructed directly from high-dimensional data (like gene
expression/RNA sequencing/methylation/brain imaging data) that
can be used in subsequent analyses to adjust for unknown,
unmodeled, or latent sources of noise. The sva package can be
used to remove artifacts in three ways: (1) identifying and
estimating surrogate variables for unknown sources of variation
in high-throughput experiments (Leek and Storey 2007 PLoS
Genetics,2008 PNAS), (2) directly removing known batch
effects using ComBat (Johnson et al. 2007 Biostatistics) and (3) removing
batch effects with known control probes (Leek 2014 biorXiv).
Removing batch effects and using surrogate variables in
differential expression analysis have been shown to reduce
dependence, stabilize error rate estimates, and improve
reproducibility, see (Leek and Storey 2007 PLoS Genetics, 2008
PNAS or Leek et al. 2011 Nat. Reviews Genetics).
Maintainer: Jeffrey T. Leek <jtleek@gmail.com>, John D. Storey
<jstorey@princeton.edu>, W. Evan Johnson <wej@bu.edu>
Depends: R (>= 2.8), mgcv, genefilter
Suggests: limma, pamr, bladderbatch, BiocStyle, zebrafishRNASeq,
testthat
License: Artistic-2.0
biocViews: Microarray, StatisticalMethod, Preprocessing,
MultipleComparison, Sequencing, RNASeq, BatchEffect,
Normalization
NeedsCompilation: yes
Packaged: 2016-05-04 04:16:38 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'sva' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include    -fpic  -g -O2  -c sva.c -o sva.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o sva.so sva.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/sva/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'sva'
    finding HTML links ... done
    ComBat                                  html  
    empirical.controls                      html  
    f.pvalue                                html  
    fstats                                  html  
    fsva                                    html  
    irwsva.build                            html  
    num.sv                                  html  
    psva                                    html  
    ssva                                    html  
    sva                                     html  
    sva.check                               html  
    svaseq                                  html  
    twostepsva.build                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (sva)
Making 'packages.html' ... done