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ABarray
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Category
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arrayMagic
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beadarraySNP
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beadarray
- fixed bug in createBeadSummaryData(). rownames are now assigned to se.exprs and NoBeads slots.
- fixed bug in plotBeadIntensities(). Changed variable name of intensities from 'I' to 'intens' and now checks that there are 1 or more items for plotting.
- fixed bug in plotBeadDensities() - when 'col' and 'arrays' was specified, lines weren't coloured correctly.
- new arguments tiffExtGrn and tiffExtRed in readIllumina() allowing user to specify tiff extensions. Previously assumed all tiffs ended in _Grn.tif or _Red.tif, however this is not always the case.
- updated readIllumina() and createBeadSummaryData() documentation

[/beadarray] permanent link

puma
Update to version 1.5.3
- changes to pumaComb and create_eset_r to fix bug when using multi-level factors
- updated documentation of pumaPCA to make clear that the default is to use 1000 probesets, not all

[/puma] permanent link

nnNorm
Removed psfig from \usepackage{} in the .Rnw file of the following packages: MeasurementError.cor, GEOquery, rama, marray, aCGH, multtest, nnNorm, RMAGEML, ACME and bridge. Psfig/TeX was actually not needed by these vignettes. Besides Psfig/TeX has licensing issues and will be removed from our build machines.

[/nnNorm] permanent link

rama
Removed psfig from \usepackage{} in the .Rnw file of the following packages: MeasurementError.cor, GEOquery, rama, marray, aCGH, multtest, nnNorm, RMAGEML, ACME and bridge. Psfig/TeX was actually not needed by these vignettes. Besides Psfig/TeX has licensing issues and will be removed from our build machines.

[/rama] permanent link

multtest
Removed psfig from \usepackage{} in the .Rnw file of the following packages: MeasurementError.cor, GEOquery, rama, marray, aCGH, multtest, nnNorm, RMAGEML, ACME and bridge. Psfig/TeX was actually not needed by these vignettes. Besides Psfig/TeX has licensing issues and will be removed from our build machines.

[/multtest] permanent link

flowCore
Updated with new gatingML gates.
Updated with new gatingML gates.

[/flowCore] permanent link

aCGH
Removed psfig from \usepackage{} in the .Rnw file of the following packages: MeasurementError.cor, GEOquery, rama, marray, aCGH, multtest, nnNorm, RMAGEML, ACME and bridge. Psfig/TeX was actually not needed by these vignettes. Besides Psfig/TeX has licensing issues and will be removed from our build machines.

[/aCGH] permanent link

RMAGEML
Removed psfig from \usepackage{} in the .Rnw file of the following packages: MeasurementError.cor, GEOquery, rama, marray, aCGH, multtest, nnNorm, RMAGEML, ACME and bridge. Psfig/TeX was actually not needed by these vignettes. Besides Psfig/TeX has licensing issues and will be removed from our build machines.

[/RMAGEML] permanent link

ACME
Removed psfig from \usepackage{} in the .Rnw file of the following packages: MeasurementError.cor, GEOquery, rama, marray, aCGH, multtest, nnNorm, RMAGEML, ACME and bridge. Psfig/TeX was actually not needed by these vignettes. Besides Psfig/TeX has licensing issues and will be removed from our build machines.

[/ACME] permanent link

bridge
Removed psfig from \usepackage{} in the .Rnw file of the following packages: MeasurementError.cor, GEOquery, rama, marray, aCGH, multtest, nnNorm, RMAGEML, ACME and bridge. Psfig/TeX was actually not needed by these vignettes. Besides Psfig/TeX has licensing issues and will be removed from our build machines.

[/bridge] permanent link

GEOquery
Removed psfig from \usepackage{} in the .Rnw file of the following packages: MeasurementError.cor, GEOquery, rama, marray, aCGH, multtest, nnNorm, RMAGEML, ACME and bridge. Psfig/TeX was actually not needed by these vignettes. Besides Psfig/TeX has licensing issues and will be removed from our build machines.

[/GEOquery] permanent link

marray
Removed psfig from \usepackage{} in the .Rnw file of the following packages: MeasurementError.cor, GEOquery, rama, marray, aCGH, multtest, nnNorm, RMAGEML, ACME and bridge. Psfig/TeX was actually not needed by these vignettes. Besides Psfig/TeX has licensing issues and will be removed from our build machines.

[/marray] permanent link

xcms
Standardised peak area calculation by introducing scan-distance multiplier to findPeaks.centWave()

[/xcms] permanent link

MeasurementError.cor
Removed psfig from \usepackage{} in the .Rnw file of the following packages: MeasurementError.cor, GEOquery, rama, marray, aCGH, multtest, nnNorm, RMAGEML, ACME and bridge. Psfig/TeX was actually not needed by these vignettes. Besides Psfig/TeX has licensing issues and will be removed from our build machines.

[/MeasurementError.cor] permanent link