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 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Updates to aroma.affymetrix - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Updates to aroma.core - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Updates to R.filesets - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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. You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/. 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