Added the MSnbase package to the repository.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSnbase@54004 bc3139a8-67e5-0310-9ffc-ced21a209358
CHANGES IN VERSION 0.99.2
-------------------------
 o updated references in package Rd <2011-03-24 Thu>
 o added readIspyData.Rd  <2011-03-24 Thu>
 o removed old readMzXMLData function <2011-03-24 Thu>
 o cleaning up code <2011-03-24 Thu>
 o fixed MSnSet initialize: setting experimentData as MIAPE <2011-03-25 Fri>
 o fixed MSnSet initialize: identical featureNames in assayData and 
   featureData for empty MSnExp istances <2011-03-25 Fri>
 o better test organisation and added object validity tests <2011-03-25 Fri>
 o updated readIspyData function <2011-03-25 Fri>




git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSnbase@54059 bc3139a8-67e5-0310-9ffc-ced21a209358
Deleted pdf vignettes from repository

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSnbase@54060 bc3139a8-67e5-0310-9ffc-ced21a209358
Switched from pdfSweave to Sweave to build on lamb1

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSnbase@54113 bc3139a8-67e5-0310-9ffc-ced21a209358
Removed pdfSweave from Suggests field.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSnbase@54457 bc3139a8-67e5-0310-9ffc-ced21a209358
Bumped version numbers for BioC 2.8 release.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSnbase@54800 bc3139a8-67e5-0310-9ffc-ced21a209358
Bumped version numbers again for new BioC 2.9 devel cycle.

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSnbase@54802 bc3139a8-67e5-0310-9ffc-ced21a209358
Commited changes made during devel-release transition - see NEWS for v1.1.1

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSnbase@54883 bc3139a8-67e5-0310-9ffc-ced21a209358
Quantification by trapezoidation now has strict argument. Removed many warnings in quantify. Updated vignette with illustrative plots for quantitation methods and spectrum pre-processing. See NEWS for more details.



git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSnbase@55087 bc3139a8-67e5-0310-9ffc-ced21a209358
exporting as.data.frame.Spectrum and coerce to return a Spectrum's mz and intensity as data.frame.


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSnbase@55097 bc3139a8-67e5-0310-9ffc-ced21a209358
Added combineFeatures function that summerised/aggregates features in an MSnSet. 


git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSnbase@55246 bc3139a8-67e5-0310-9ffc-ced21a209358
added combineFeatures example in demo vignette

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSnbase@55274 bc3139a8-67e5-0310-9ffc-ced21a209358
added incomplete dissociation and spectral counting sections to demo vignette and mention bio-sig-proteomics list

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSnbase@55300 bc3139a8-67e5-0310-9ffc-ced21a209358
fixed typo in vignette foreword

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSnbase@55303 bc3139a8-67e5-0310-9ffc-ced21a209358
added/documented MSnSet purity correction method

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSnbase@55356 bc3139a8-67e5-0310-9ffc-ced21a209358
new makeImpuritiesMatrix, itraqdata and writeMgfData

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSnbase@55442 bc3139a8-67e5-0310-9ffc-ced21a209358
updated and exported normalise method and vignette updates

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSnbase@55561 bc3139a8-67e5-0310-9ffc-ced21a209358
misc minor fixes/typos, added plot parameter to plot methods, new meanSdPlot method

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSnbase@55646 bc3139a8-67e5-0310-9ffc-ced21a209358
new vignette sections (customising plots and QC), plot2D and plotDensity, preprocSelection[Table]

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSnbase@55883 bc3139a8-67e5-0310-9ffc-ced21a209358
centroided MSnExp plotting

git-svn-id: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MSnbase@56096 bc3139a8-67e5-0310-9ffc-ced21a209358