[BioC] Release of Bioconductor 1.3

[A.J. Rossini]

The Bioconductor core group would like to announce the 1.3 release of
the Bioconductor software.  There are many new packages as well as
several major upgrades and fixes in older packages, and users are
encouraged to check them out.  Release 1.3 is intended to be operated
with R version 1.8.X, which can be obtained at CRAN
(http://cran.r-project.org/) 


-- WHAT FEATURES DOES THIS RELEASE PROVIDE?

All packages from the 1.2 release are included.  All current bug fixes
have been applied, and most have upgraded and provide enhanced
functionality.

-- NEW PACKAGES AND MAJOR UPGRADES FOR RELEASE 1.3 --

The following is an overview of the most important changes, additions,
and upgrades:

--- affy

   There have been many improvements to the affy package.  There were
   big speed and memory improvement of ReadAffy, read.affybatch,
   justRMA.  A mas5calls method was added to get Affymetrix's P/M/A
   calls.  Cel and Cdf classes are no longer supported. Function,
   read.celfile and other Cel related methods and functions
   removed. Most Cdf related functions have moved to the makecdfenv
   package.  Function read.probematrix added. It reads CEL files and
   returns a matrix of PM, MM, or both. This function is more memory
   efficient than read.affybatch.  Also, affy no longer depends on the
   affydata package. For this reason some examples have been moved
   from affy vignettes to the affydata vignette.  The previously
   deprecated express function has been completely removed.  Lastly,
   most normalization routines for AffyBatches can now be called with
   the parameter type which specifies whether the normalization should
   be applied as a PM-only, MM-only, both PM and MM together or PM and
   MM separately.

--- affycomp:

   New assessment was added: assessSpikeIn2. Examples of new feature:
Local 
   slopes are computes and ROC curves divided by overall expression.
   Also, all functions that work for hgu95a spike in now also work for
hgu133a
   spike in experiment

--- annaffy:

   Functions for handling data from Bioconductor Affymetrix annotation
   data packages. Produces compact HTML and text reports including
   experimental data and URL links to many online databases. Allows
   searching biological metadata using various criteria.

--- Biobase:

   The generic function as.data.frame() now works on objects of class
   exprSet.  This lets one access the extensive modeling facilities
   through formula offered by R and packages like 'nlm'.

--- factDesign:

   A package containing functions useful for analyzing data from
   factorial designed microarray experiments.

--- gpls:

   Classification using partial least squares (PLS), a popular
   dimension reduction tool in chemometrics, in the context of
   generalized linear regression based on a previous approach,
   Iteratively ReWeighted Partial Least Squares (IRWPLS) by Marx
   (1996).  Both two-group and multi-group classifications are
   incorporated. Firth's bias reduction procedure is also incorporated
   to ensure more stable and finite regression coefficients.

--- graph, Rgraphviz, and RBGL:

   Graph/Network handling is greatly improved. There is tighter
   integration between graph, RBGL and Rgraphviz. Colors and SubGraph
   layouts are now supported in Rgraphviz. RBGL support includes
   minimal spanning trees, both strong and weakly connected
   components, and Dijkstra's shortest path algorithm.  In graph,
   enhancements in validity checking and representation have been
   made. New classes have been established that will allow for general
   representations of nodes and edges. Capabilities include adding or
   deleting both nodes and edges, combining sets of nodes into a
   single node. Unions, intersections and complements of graphs
   defined on a common set of nodes. Joining of two graphs into a
   single graph. Functions to compute indegree and outdegree. 

--- limma:

   Substantial updates including support for more image analysis
   programs, new background correction methods, single channel
   normalization, support for import of exprSet and marrayNorm data
   objects, improved support for design and contrast matrices, new
   fitted model object class, within-gene multiple testing, Venn
   diagrams and generally a move to a simpler command style at the
   user level.

--- matchprobes:

   A new package providing tools for working with probe sequence
   information: calculate ATCG content, reverse, complement, mismatch
   sequences; fast exact sequence matching; combine AffyBatches of
   different chip types; create probe data packages.  

--- Measurement.cor:

   A package to fit a two-level measurement error model for estimation
   of correlation coefficient between two random variables assuming
   bivariate normality for both the true value and measurement
   error. This model allows dependence between measurement errors
   hence is more flexible.

--- ontoTools:

   Software for working with ontologies (structured vocabularies) and
   their associations with general data resources. 

--- Rdbi, RdbiPgSQL:

   Generic framework for database access in R. Adapted from Rdbi
   authored by Timothy H. Keitt, with methods for accessing data
   stored in PostgreSQL tables (Adapted from Rdbi.PgSQL, authored
   by Timothy H. Keitt)

--- SNPtools:

   Currently an interface to the SNPper data resource maintained at
   Childrens' Boston, which curates SNP-related data from a variety of
   sources.

--- splicegear:

   A new package that works with oligonucleotide microarrays designed
   to monitor or confirm the existence of splice variants.  It can
   extract simple splice-variant information in XML format.  This is
   demonstrated by the connectivity to an existing database of
   putative splice variants.  The package can also integrate easily
   with the results obtained from the package 'matchprobes'. 

--- vsn:

   Two new functions were added 'sagmbSimulateData' and 'sagmbAssess'
   to quantitatively verify finite sample properties and outlier
   robustness of the parameter estimation in vsn(). 

-- TOOLS:

The released packages include tools which facilitate:

* annotation (AnnBuilder, annotate).

* data management and organization through the use of the S4 class
  structure (Biobase, marrayClasses, limma).   

* identification of differentially expressed genes and clustering 
  (edd, genefilter, geneplotter, multtest, ROC, limma)

* analysis of Affymetrix expression array data (affy, affycomp,
  gcrma)

* diagnostic plots and normalization for cDNA array data (marrayInput,
  marrayNorm, marrayPlots)

* storage and retrieval of large datasets (rhdf5, externalVector,
   Rdbi, RdbiPgSQL).

* facilitate user interaction (tkWidgets, widgetTools)

There are currently a total of 48 packages, not including precomputed
annotation data packages for Affymetrix GeneChips(tm), KEGG, GO,
and LocusLink mappings.


-- HELP AND RESOURCES:

The packages and more details may be found on the Bioconductor WWW
site: 

      http://www.bioconductor.org/

Information on subscribing to the mailing list and viewing its
archives
can be found at:

      http://www.stat.math.ethz.ch/mailman/listinfo/bioconductor

Please use that list to discuss Bioconductor specific issues, bugs,
and problems.  Note that every package has a vignette (a literate
program which provides an annotated example of the package's use) as
well as possibly some "HOWTO"s.  These document the tool's usage, and
are provided in the "doc" subdirectory of each package library.


-- WHO:

For the Bioconductor development team:

Douglas Bates, University of Wisconsin, USA.
Ben Bolstad, Division of Biostatistics, UC Berkeley, USA.
Vince Carey, Harvard Medical School, USA.
Marcel Dettling, Federal Inst. Technology, Switzerland.
Sandrine Dudoit, Division of Biostatistics, UC Berkeley, USA.
Byron Ellis, Harvard Department of Statistics, USA.
Laurent Gautier, Technial University of Denmark, Denmark.
Robert Gentleman, Harvard Medical School, USA.
Jeff Gentry, Dana-Farber Cancer Institute, USA.
Kurt Hornik, Technische Universitat Wien, Austria.
Torsten Hothorn, Institut fuer Medizininformatik,
        Biometrie und Epidemiologie, Germany.
Wolfgang Huber, DKFZ Heidelberg, Molecular Genome Analysis, Germany.
Stefano Iacus, Italy
Rafael Irizarry, Department of Biostatistics (JHU), USA.
Friedrich Leisch, Technische Universitat Wien, Austria.
Martin Maechler, Federal Inst. Technology, Switzerland.
Colin Smith, Scripps Research Institute, USA.
Gordon Smyth, Walter and Eliza Hall Institute, Australia.
Anthony Rossini, University of Washington
        and the Fred Hutchinson Cancer Research Center, USA.
Gunther Sawitzki, Institute fur Angewandte Mathematik, Germany.
Luke Tierney, University of Iowa, USA.
Jean Yee Hwa Yang, University of California, San Francisco, USA.
Jianhua (John) Zhang, Dana-Farber Cancer Institute, USA.


-- 
rossini at u.washington.edu            http://www.analytics.washington.edu/ 
Biomedical and Health Informatics   University of Washington
Biostatistics, SCHARP/HVTN          Fred Hutchinson Cancer Research Center
UW (Tu/Th/F): 206-616-7630 FAX=206-543-3461 | Voicemail is unreliable
FHCRC  (M/W): 206-667-7025 FAX=206-667-4812 | use Email

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