[med-svn] [r-bioc-limma] 02/03: Merge tag 'upstream/3.18.0_dfsg'

[Charles Plessy]

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

commit e77d8aaee36ee28380a2bc57a560276293c625fc
Merge: 2aa5678 5c7fc4d
Author: Charles Plessy <plessy at debian.org>
Date:   Wed Oct 16 14:29:32 2013 +0900

    Merge tag 'upstream/3.18.0_dfsg'
    
    Upstream version 3.18.0~dfsg
    
    # gpg: Signature made Wed 16 Oct 2013 14:29:26 JST using RSA key ID B3443334
    # gpg: Good signature from "Charles Plessy <plessy at riken.jp>"

 DESCRIPTION                 |   12 +--
 NAMESPACE                   |    4 +
 R/alias2Symbol.R            |    6 +-
 R/beadCountWeights.R        |   99 +++++++++++++++++
 R/contrastAsCoef.R          |   26 +++++
 R/genas.R                   |  228 +++++++++++++++++++++------------------
 R/geneset-roast.R           |   27 ++---
 R/lmfit.R                   |   98 ++++++++++++-----
 R/loessFit.R                |   50 ++++-----
 R/norm.R                    |    4 +-
 R/plots-ma.R                |  251 ++++++++++++++++++++++++++-----------------
 R/predFCm.R                 |    2 +-
 R/read-ilmn.R               |   36 +++++--
 R/subsetting.R              |    3 +-
 R/toptable.R                |  184 +++++++++++++++++++++----------
 R/treat.R                   |   63 ++++++++---
 build/vignette.rds          |  Bin 0 -> 219 bytes
 inst/doc/changelog.txt      |  180 +++++++++++++++++++++++++++----
 inst/doc/limma.R            |    2 -
 inst/doc/limma.pdf          |  Bin 45597 -> 45597 bytes
 man/01Introduction.Rd       |    3 +-
 man/06linearmodels.Rd       |    3 +-
 man/asmalist.Rd             |    7 ++
 man/beadCountWeights.Rd     |   61 +++++++++++
 man/contrastAsCoef.Rd       |   48 +++++++++
 man/contrasts.fit.Rd        |    2 +-
 man/ebayes.Rd               |   15 ++-
 man/fitfdist.Rd             |    4 +-
 man/genas.Rd                |   88 ++++++++++-----
 man/getEAWP.Rd              |    8 +-
 man/lmFit.Rd                |    3 +
 man/loessfit.Rd             |   86 +++++++++------
 man/plotma.Rd               |    9 +-
 man/predFCm.Rd              |    1 +
 man/propTrueNull.Rd         |    1 +
 man/removeBatchEffect.Rd    |    4 +-
 man/roast.Rd                |    1 +
 man/squeezeVar.Rd           |   23 +++-
 man/targetsA2C.Rd           |    2 +-
 man/toptable.Rd             |   15 ++-
 src/normexp.c               |    4 +-
 tests/limma-Tests.R         |   13 ++-
 tests/limma-Tests.Rout.save |  229 +++++++++++++++++++++++----------------
 43 files changed, 1347 insertions(+), 558 deletions(-)

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