[med-svn] [r-bioc-limma] branch upstream updated (eab8baa -> 3913647)

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a change to branch upstream
in repository r-bioc-limma.

      from  eab8baa   Imported Upstream version 3.18.1~dfsg
       new  3913647   Imported Upstream version 3.18.4+dfsg

The 1 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails.  The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.


Summary of changes:
 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(-)
 rename R/{plotFG.R => plotFB.R} (51%)
 copy inst/doc/{limma.Rnw => intro.Rnw} (89%)
 mode change 100755 => 100644
 rename inst/doc/{limma.pdf => intro.pdf} (73%)
 rename inst/doc/limma.Rnw => vignettes/intro.Rnw (89%)
 mode change 100755 => 100644

-- 
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