[med-svn] [r-bioc-limma] 02/07: Merge tag 'upstream/3.18.4+dfsg'

[Andreas Tille]

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tille pushed a commit to branch master
in repository r-bioc-limma.

commit b8d0515880b8f55b6894b2c9f4a1d3584e069d60
Merge: 9ec05b1 3913647
Author: Andreas Tille <tille at debian.org>
Date:   Sat Dec 7 10:13:39 2013 +0100

    Merge tag 'upstream/3.18.4+dfsg'
    
    Upstream version 3.18.4+dfsg

 DESCRIPTION                               |   6 +-
 NAMESPACE                                 |   8 ++
 R/dups.R                                  |  36 +++--
 R/genas.R                                 |  91 ++++++-------
 R/{plotFG.R => plotFB.R}                  |  24 +++-
 R/plotdensities.R                         | 211 +++++++++++++-----------------
 R/plots-ma.R                              |  10 +-
 R/read-ilmn.R                             |   3 +-
 R/squeezeVar.R                            |  23 +++-
 R/toptable.R                              |   6 +-
 build/vignette.rds                        | Bin 219 -> 229 bytes
 inst/doc/changelog.txt                    |  46 +++++++
 inst/doc/index.html                       |   3 +-
 inst/doc/{limma.Rnw => intro.Rnw}         |   6 +-
 inst/doc/{limma.pdf => intro.pdf}         | Bin 45597 -> 46191 bytes
 man/09Diagnostics.Rd                      |   2 +-
 man/EList.Rd                              |   6 +-
 man/auROC.Rd                              |  12 +-
 man/avereps.Rd                            |  16 ++-
 man/backgroundcorrect.Rd                  |   6 +-
 man/beadCountWeights.Rd                   |  35 ++++-
 man/nec.Rd                                |   9 +-
 man/normalizebetweenarrays.Rd             |   2 +-
 man/plotDensities.Rd                      | 102 +++++----------
 man/plotFB.Rd                             |  14 +-
 man/read.ilmn.Rd                          |  30 +++--
 man/voom.Rd                               |   1 +
 man/vooma.Rd                              |   1 +
 inst/doc/limma.Rnw => vignettes/intro.Rnw |   6 +-
 29 files changed, 397 insertions(+), 318 deletions(-)

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