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commit 1cd47356b3f9e5ad8feb74e065f6cabb11ff993f Merge: 00175e1 decb5cf Author: Gordon Ball <[email protected]> Date: Tue Jun 21 15:17:16 2016 +0200 Merge tag 'upstream/3.28.10+dfsg' Upstream version 3.28.10+dfsg 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(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/r-bioc-limma.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
