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commit 8e8ae7024aab7a0a47fb98e58e95c33dce707ac9 Merge: 871896f 802f308 Author: Andreas Tille <ti...@debian.org> Date: Sun Jul 19 18:14:11 2015 +0200 Merge tag 'upstream/3.24.13+dfsg' Upstream version 3.24.13+dfsg DESCRIPTION | 15 +- NAMESPACE | 18 +- R/alias2Symbol.R | 28 ++- R/arrayWeights.R | 7 +- R/auROC.R | 55 +++++ R/background-normexp.R | 6 +- R/classes.R | 2 +- R/dups.R | 8 +- R/fitFDistRobustly.R | 6 +- R/genas.R | 19 +- R/geneset-camera.R | 11 +- R/geneset-fry.R | 138 ++++++++++++ R/geneset-ids2indices.R | 14 ++ R/geneset-roast.R | 14 +- R/geneset-romer.R | 435 +++++++++++++++----------------------- R/goana.R | 221 +++++++++++-------- R/kegga.R | 277 ++++++++++++++++++++++++ R/lmfit.R | 35 +-- R/loessFit.R | 10 +- R/neqc.R | 22 +- R/norm.R | 24 ++- R/plot.R | 64 ------ R/plotMD.R | 116 ++++++++++ R/plotMDS.R | 80 ++++--- R/plotWithHighlights.R | 56 ++--- R/plotdensities.R | 40 ++-- R/plots-ma.R | 18 +- R/predFCm.R | 80 +++---- R/read.idat.R | 24 ++- R/roc.R | 20 -- R/sepchannel.R | 6 +- R/squeezeVar.R | 4 +- R/toptable.R | 3 +- R/venn.R | 73 +++++-- R/voom.R | 6 +- R/write.R | 17 +- build/vignette.rds | Bin 230 -> 231 bytes inst/CITATION | 25 ++- inst/NEWS.Rd | 113 ++++++++++ inst/doc/changelog.txt | 297 ++++++++++++++++++++++++-- inst/doc/intro.pdf | Bin 46191 -> 46191 bytes man/01Introduction.Rd | 20 +- man/02classes.Rd | 15 ++ man/03reading.Rd | 14 ++ man/04Background.Rd | 15 ++ man/05Normalization.Rd | 15 ++ man/06linearmodels.Rd | 18 ++ man/07SingleChannel.Rd | 15 ++ man/08Tests.Rd | 14 ++ man/09Diagnostics.Rd | 36 +++- man/10GeneSetTests.Rd | 34 ++- man/11RNAseq.Rd | 32 ++- man/EList.Rd | 1 + man/arrayWeights.Rd | 2 +- man/arrayWeightsQuick.Rd | 2 +- man/asmalist.Rd | 4 +- man/auROC.Rd | 14 +- man/backgroundcorrect.Rd | 4 +- man/barcodeplot.Rd | 25 ++- man/decideTests.Rd | 7 +- man/diffSplice.Rd | 4 +- man/ebayes.Rd | 8 +- man/genas.Rd | 10 + man/getEAWP.Rd | 2 +- man/goana.MArrayLM.Rd | 89 -------- man/goana.Rd | 111 ++++++++-- man/imageplot.Rd | 2 +- man/lmFit.Rd | 7 +- man/malist.Rd | 2 +- man/mdplot.Rd | 40 ++-- man/modifyWeights.Rd | 2 +- man/normalizeRobustSpline.Rd | 14 +- man/normalizeWithinArrays.Rd | 2 +- man/normalizebetweenarrays.Rd | 2 +- man/normexpfit.Rd | 6 +- man/normexpsignal.Rd | 6 +- man/plot.Rd | 94 -------- man/plotDensities.Rd | 12 +- man/plotExons.Rd | 2 +- man/plotMD.Rd | 133 ++++++++++++ man/plotMDS.Rd | 34 +-- man/plotSplice.Rd | 5 +- man/plotWithHighlights.Rd | 96 +++++++++ man/plotma.Rd | 49 +++-- man/plotma3by2.Rd | 2 + man/predFCm.Rd | 59 +++--- man/propTrueNull.Rd | 7 +- man/rankSumTestwithCorrelation.Rd | 5 +- man/read.idat.Rd | 9 +- man/read.maimages.Rd | 7 + man/readGPRHeader.Rd | 8 +- man/readImaGeneHeader.Rd | 2 +- man/readgal.Rd | 2 +- man/rglist.Rd | 2 +- man/roast.Rd | 29 ++- man/romer.Rd | 34 +-- man/topGO.Rd | 24 ++- man/topSplice.Rd | 4 +- man/toptable.Rd | 8 + man/venn.Rd | 9 +- man/voom.Rd | 11 +- man/voomWithQualityWeights.Rd | 34 +-- man/vooma.Rd | 2 +- src/weighted_lowess.c | 80 ++++--- tests/limma-Tests.R | 13 +- tests/limma-Tests.Rout.save | 229 ++++++++++++-------- vignettes/intro.Rnw | 49 +++++ 107 files changed, 2802 insertions(+), 1253 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 debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit