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 140fe49 Imported Upstream version 3.22.1+dfsg new 802f308 Imported Upstream version 3.24.13+dfsg new 3fc04a1 Imported Upstream version 3.24.14+dfsg new 7a403fe Imported Upstream version 3.24.14+dfsg new 1411fa9 Imported Upstream version 3.24.14+dfsg The 4 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 | 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 | 52 +++-- R/geneset-fry.R | 138 ++++++++++++ R/geneset-ids2indices.R | 14 ++ R/geneset-roast.R | 16 +- R/geneset-romer.R | 435 +++++++++++++++----------------------- R/goana.R | 221 +++++++++++-------- R/kegga.R | 277 ++++++++++++++++++++++++ R/lmfit.R | 39 ++-- 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/subsetting.R | 16 +- 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 | 315 +++++++++++++++++++++++++-- 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/TestResults.Rd | 5 +- 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/camera.Rd | 8 +- 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 | 31 +-- man/romer.Rd | 34 +-- man/summary.Rd | 2 +- 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 | 163 +++++++------- 110 files changed, 2757 insertions(+), 1281 deletions(-) create mode 100755 R/auROC.R create mode 100644 R/geneset-fry.R create mode 100644 R/geneset-ids2indices.R create mode 100644 R/kegga.R delete mode 100644 R/plot.R create mode 100644 R/plotMD.R delete mode 100755 R/roc.R delete mode 100644 man/goana.MArrayLM.Rd delete mode 100644 man/plot.Rd create mode 100644 man/plotMD.Rd create mode 100644 man/plotWithHighlights.Rd -- 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