[BioC] ANN: Bioconductor Release 1.7 is available

[Seth Falcon]

We are pleased to announce the release of Bioconductor 1.7.  This
release includes 17 new packages and many improvements and bug fixes
to existing packages.

Please visit http://www.bioconductor.org for details and downloads.

Contents
========

- Release Highlights
- Getting Started With Bioconductor 1.7
- Known Issues
- 17 New Packages


Release Highlights
==================

- Rgraphviz is now available as a binary package for Windows

- Annotation data packages now include protein information from IPI
  (see the PFAM and PROSITE environments in the data packages).


Getting Started With Bioconductor 1.7
=====================================

To get started with Bioconductor 1.7, please:

- Install R 2.2.0.  Bioconductor 1.7 has been designed expressly for
  this version of R.

- Follow the instructions here:
  http://www.bioconductor.org/docs/install-howto.html


Known Issues
============

- The following packages are not currently available for Windows:
      affxparser    biomaRt       GeneR         GeneTraffic
      iSPlot        KEGGSOAP      maDB          MANOR
      msbase        pgUtils       RdbiPgSQL     rhdf5
      RMAGEML       SAGElyzer     SBMLR         stam
      widgetInvoke 

- The following packages are not currently available for OS X:
      aCGH          edd           RdbiPgSQL     rhdf5
      RMAGEML       xcms

- The genbank() function in package annotate is broken.  The CGI
  script it was accessing at NCBI appears not to be functioning.  You
  will see a message like::

      parser error : Start tag expected, '<' not found
      Content-Type: text/html; charset=UTF-8

- The hexbin package is unable to execute its vignette on Windows.  A
  plot method fails giving an error message about -Inf, Inf xlim. 

- The golubEsets dataset is temporarily unavailable, it will be fixed
  next week.


17 New Packages
===============

affxparser
Title: Affymetrix File Parsing SDK
Author: James Bullard, Kasper Daniel Hansen

affyQCReport
Title: QC Report Generation for affyBatch objects
Author: Craig Parman, Conrad Halling

clusterStab
Title: Compute cluster stability scores for microarray data
Author: James W. MacDonald, Debashis Ghosh, Mark Smolkin

diffGeneAnalysis
Title: Performs differential gene expression Analysis
Author: Choudary Jagarlamudi

externalVector
Title: Vector objects for R with external storage
Author: Saikat DebRoy

fdrame
Title: FDR adjustments of Microarray Experiments (FDR-AME)
Author: Yoav Benjamini, Effi Kenigsberg, Anat Reiner, Daniel Yekutieli

GlobalAncova
Title: Calculates a global test for differential gene expression
Author: U. Mansmann, R. Meister

HEM
Title: Heterogeneous error model for identification of differentially expressed genes under multiple conditions
Author: HyungJun Cho

maSigPro
Title: Significant Gene Expression Profile Differeneces in Time Course Microarray Data
Author: Ana Conesa, Maria José Nueda

maanova
Title: Tools for analyzing Micro Array experiments
Author: Hao Wu <hao at jax.org>, with ideas from Gary Churchill, Katie Kerr and Xiangqin Cui

MANOR
Title: Micro-Array NORmalization
Author: Pierre Neuvial, Philippe Hupé

mmgmos
Title: multi-chip modified gamma Model of Oligonucleotide Signal
Author: Xuejun Liu, Magnus Rattray, Marta Milo, Neil D. Lawrence

pdmclass
Title: Classification of Microarray Samples using Penalized Discriminant Methods
Author: James W. MacDonald, Debashis Ghosh, based in part on 

reb
Title: Regional Expression Biases
Author: Kyle A. Furge and Karl Dykema

simulatorAPMS
Title: Computationally simulates the AP-MS technology.
Author: Tony Chiang <tchiang at fhcrc.org>

SBMLR
Title: SBML-R Interface and Analysis Tools
Author: Tomas Radivoyevitch

timecourse
Title: Statistical Analysis for Developmental Microarray Time Course Data
Author: Yu Chuan Tai 


Best Wishes,

+ seth
For the Bioconductor Core Team