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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