[aroma.affymetrix] aroma.affymetrix v1.8.0 released

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[aroma.affymetrix] aroma.affymetrix v1.8.0 released

Henrik Bengtsson-4
Hi all,

aroma.affymetrix v1.8.0 and friends have been released and is being
rolled out on CRAN as we speak.  It is highly recommended to update:

source("http://aroma-project.org/hbLite.R");
hbInstall("aroma.affymetrix");

This update follows the September releases of R v2.12.0 and
Bioconductor v2.8, which we also recommended to be used with the aroma
framework.

What's new?  Software robustness, software robustness, and software
robustness!  Not that we're doing badly before but there are always
some pot holes out there and the aroma framework tries it best so you
won't hit them.   Other significant improvements is that the gcRMA
pipeline now support more chip types and utilizes our generic aroma
cell sequence annotation files.  Moreover, for segmentation models
such as CbsModel() it is now possible specify all parameters accepted
by the underlying segmentation model in the constructor, e.g.
CbsModel(..., min.width=5, alpha=0.05).  Details on updates are listed
below.

Documentation keeps getting added to the http://www.aroma-project.org/
website.  As before, any kind of contribution to it is greatly
appreciated.

Cheers,

Henrik & co-developers


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Updates to aroma.affymetrix
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Version: 1.8.0 [2010-11-07]
o Committed to CRAN. No updates.


Version: 1.7.4 [2010-11-04]
o ROBUSTNESS: Bumping the required versions of the dependent package
  in order to make sure we are not affected by old bugs.


Version: 1.7.3 [2010-10-02]
o Now doGCRMA() automagically makes sure that the default CDF is used
  in the QuantileNormalization step, while use a custom CDF everywhere
  else if set.  Added argument 'type' to doGCRMA() which is passed to
  QuantileNormalization().
o GENERALIZATION: Now GcRmaBackgroundCorrection(..., type="affinities")
  can process also chip types for which there are no MMs and for
  which non-specific probes are explicitly specified.
o GENERALIZATION: Now GcRmaBackgroundCorrection calculates gcRMA probe
  affinites based on Aroma Cell Sequence (ACS) annotation files.
  For backward compatibility, it turns to Affymetrix probe-tab files
  if an ACS file is not located.
o ROBUSTNESS: Added more validation of the arguments passed to
  the constructor of GcRmaBackgroundCorrection and its internal
  functions.  Also added more verbose output during processing.
o CORRECTION: The DESCRIPTION file suggested a package version that
  did not exist.


Version: 1.7.2 [2010-09-06]
o ROBUSTNESS: Added extractAffyBatch() for ChipEffectSet that gives
  an informative error message explaining why it doesn't make sense
  to do so.


Version: 1.7.1 [2010-08-14]
o Added doGCRMA() for AffymetrixCelSet and data-set names.
  doGCRMA() runs in bounded memory and replicates the results of
  gcrma() in the gcrma package with great precision.



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Updates to aroma.core
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Version: 1.8.0 [2010-11-07]
o Committed to CRAN.
o CLEANUP: Dropped non-used Javascript toolkit code that was intended
  to be used for a future version of ChromosomeExplorer.


Version: 1.7.6 [2010-11-06]
o ROBUSTNESS: Now subsample() for BinnedScatter utilizes resample().
o CLEANUP: Removed stext().  It is in R.utils.
o CLEANUP: Removed some outdated patches for R v2.7.0 and before.
o CLEANUP: Package no longer need to "suggest" geneplotter.


Version: 1.7.5 [2010-10-25]
o Now fit() for CopyNumberSegmentationModel also passed the optional
  arguments ('...') passed to the constructor function.  This makes it
  possible to specify all arguments while initiating the model, e.g.
  sm <- CbsModel(..., min.width=5, alpha=0.05).
o Now optional arguments '...' to CopyNumberChromosomalModel are recorded.


Version: 1.7.4 [2010-10-13]
o ROBUSTNESS/BUG FIX: The internal drawCytoband2() used to annotate
  chromosomal plots with cytobands tries to utilize GLAD package,
  if available.  However, even when GLAD is installed it may still be
  broken due to missing dynamic libraries, e.g. 'Error in
  library.dynam(lib, package, package.lib) : DLL 'GLAD' not found: maybe
  not installed for this architecture?'.  We now avoid this too.


Version: 1.7.3 [2010-09-12]
o Added drawDensity() for CopyNumberRegions and RawGenomicSignals.
o Added getDensity() for CopyNumberRegions which returns the
  empirical density of the mean levels weighted by the region lengths.
o Added getLength() for CopyNumberRegions, which returns a vector
  of region lengths.
o Now the ylim defaults to c(0,5) for plot() for RawCopyNumbers.
o Added basic support for operators +, - and * to RawGenomicSignals.


Version: 1.7.2 [2010-08-22]
o Added the AromaGenomeTextFile class.
o Added genome annotation file Canine,chromosomes,UGP,HB20100822.txt to
  system.file("annotationData/genomes/Canine", package="aroma.core").
o BUG FIX: annotationData/genomes/Human/Human,chromosomes.txt had
  an extra TAB on the ChrM row.


Version: 1.7.1 [2010-08-06]
o Added abstract classes SegmentationDataFile and SegmentationDataSet
  to represent segmentation data results.  Current subclasses are
  CbsSegmentationData(File|Set).
o Added more utility methods for CopyNumberRegions.



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Updates to R.filesets
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Version: 0.9.0 [2010-08-19]
o Added sortBy() to GenericDataFileSet, which sorts files either
  in a lexicographic or a mixedsort order.
o DOCUMENTATION: Added more Rd help pages.
o DOCUMENTATION: Removed any duplicated \usage{} statements from
  the Rd documentation.

--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.


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