[med-svn] [r-bioc-limma] branch upstream updated (811b74f -> decb5cf)

[Gordon Ball]

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

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

      from  811b74f   Imported Upstream version 3.26.1+dfsg
       new  decb5cf   Imported Upstream version 3.28.10+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                    |  17 +-
 NAMESPACE                      |   4 +-
 R/alias2Symbol.R               | 100 +++++--
 R/detectionPValues.R           |  41 +++
 R/diffSplice.R                 |  15 +-
 R/dups.R                       |   2 +-
 R/ebayes.R                     |  48 ++--
 R/{squeezeVar.R => fitFDist.R} |  59 +---
 R/fitFDistRobustly.R           |  66 +++--
 R/fitmixture.R                 |  48 ++++
 R/geneset-camera.R             |  11 +-
 R/geneset-fry.R                | 232 ++++++++-------
 R/geneset-roast.R              | 633 ++++++++++++++++++-----------------------
 R/geneset-romer.R              |  15 +-
 R/goana.R                      |  50 +++-
 R/kegga.R                      | 211 +++++++++-----
 R/lmEffects.R                  | 139 +++++++++
 R/lmfit.R                      |  39 ++-
 R/loessFit.R                   |   2 +-
 R/neqc.R                       |   4 +-
 R/norm.R                       |   7 +-
 R/plotrldf.R                   | 133 +++++++--
 R/propTrueNull.R               |   6 +-
 R/read-maimages.R              |   1 +
 R/read.R                       |  14 +-
 R/read.idat.R                  | 127 ++++++---
 R/sepchannel.R                 |   2 +-
 R/squeezeVar.R                 | 203 +++----------
 R/tricubeMovingAverage.R       |  15 +-
 R/voom.R                       |  15 +-
 build/vignette.rds             | Bin 230 -> 229 bytes
 inst/NEWS.Rd                   | 225 +++++++++++++++
 inst/doc/changelog.txt         | 234 ++++++++++++++-
 inst/doc/intro.pdf             | Bin 46191 -> 46191 bytes
 man/03reading.Rd               |   1 +
 man/10GeneSetTests.Rd          |   2 +-
 man/alias2Symbol.Rd            |  14 +-
 man/camera.Rd                  |  40 ++-
 man/detectionPValue.Rd         |  58 ++++
 man/dupcor.Rd                  |  40 ++-
 man/ebayes.Rd                  |  14 +-
 man/fitfdist.Rd                |  28 +-
 man/fitmixture.Rd              |  66 +++++
 man/fitted.MArrayLM.Rd         |   5 +-
 man/getEAWP.Rd                 |  25 +-
 man/gls.series.Rd              |   4 +-
 man/goana.Rd                   |  53 +++-
 man/ids2indices.Rd             |   6 +-
 man/lmFit.Rd                   |   2 +-
 man/logcosh.Rd                 |  26 ++
 man/marraylm.Rd                |   1 +
 man/nec.Rd                     |   1 +
 man/plotRLDF.Rd                |  70 +++--
 man/propexpr.Rd                |  44 ++-
 man/read.idat.Rd               |  77 +++--
 man/read.maimages.Rd           |   3 +-
 man/removeext.Rd               |  13 +-
 man/roast.Rd                   |  63 ++--
 man/romer.Rd                   |   5 +-
 man/squeezeVar.Rd              |  10 +-
 man/targetsA2C.Rd              |   6 +
 man/venn.Rd                    |  22 +-
 man/voom.Rd                    |  12 +-
 tests/limma-Tests.R            |   4 +
 tests/limma-Tests.Rout.save    |  81 ++++--
 65 files changed, 2326 insertions(+), 1188 deletions(-)
 create mode 100644 R/detectionPValues.R
 copy R/{squeezeVar.R => fitFDist.R} (66%)
 create mode 100644 R/fitmixture.R
 create mode 100644 R/lmEffects.R
 create mode 100644 man/detectionPValue.Rd
 create mode 100644 man/fitmixture.Rd
 create mode 100644 man/logcosh.Rd

-- 
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