Hi all,
aroma.affymetrix and friends have been updated. It is highly
recommended to update:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
As usual, we have run lots of redundancy tests - a 24 hour task - to
assert that things are backward compatible, everything works as
expected, and that we get the same estimates/results as with previous
versions.
Although this release does not contain lots of new features, under the
hood we are making things more and more independent of technology,
i.e. we are preparing for supporting other platforms than Affymetrix.
The new release, adds additional protection against errors entering
your analysis, e.g. when a sysadm, a user or a power failures
interrupting the analysis while results are written to file. We have
trimmed the memory usage further for some analyzes. Another update is
that it is now possible to generate ChromosomeExplorer reports without
having to install the GLAD package (recently GLAD became trickier to
install). As usual, there were some rather minor bug fixes as well.
Cheers,
Henrik & co-developers
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Updated to aroma.affymetrix
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Version: 1.5.0 [2010-02-22]
o Submitted to CRAN. No changes since v1.4.9.
o Package passes R CMD check on R v2.10.1 patch and R v2.11.0 devel.
o Package passes all redundancy tests.
Version: 1.4.9 [2010-02-22]
o Added AromaCellCpgFile.
o Added test script for AromaCellCpgFile and AromaCellPostionFile.
o BUG FIX: The settings in 'aromaSettings' loaded by aroma.core was
overridden by defaults settings of aroma.affymetrix, even if they
already existed.
Version: 1.4.8 [2010-02-21]
o ROBUSTNESS: Now updateUnits() of ChipEffectSet updates the files in
lexicographic order. Before there was a risk that this was not done
if fullname translators are changing the lexicographic ordering.
o MEMORY OPTIMIZATION: Now updateUnits() of ChipEffectSet cleans out the
temporary data object extracted for each chip-effect file written.
It also calls the garbage collector after each file written.
o Added verbose output to updateUnits() of ProbeAffinityFile.
Version: 1.4.7 [2010-02-16]
o MEMORY OPTIMIZATION: Now process() of AllelicCrosstalkCalibration
clears the in-memory cache when finished.
o MEMORY OPTIMIZATION: Now AbstractProbeSequenceNormalization classes
cleans out more unneeded objects.
o MEMORY OPTIMIZATION: Now doCRMAv2() removes as much as possible.
o BUG FIX: readDataUnitChromosomePosition() of AffymetrixNetAffxCsvFile
failed to map chromosome 'MT' to 25. This bug was introduced
in aroma.affymetrix v1.0.7.
Version: 1.4.6 [2010-02-13]
o Added an internal version of doCRMAv2().
o BUG FIX: exportTotalAndFracB() of SnpChipEffectSet returned all arrays
in the output data set directory and not only the ones part of the
input data set.
Version: 1.4.5 [2010-02-10]
o Added redundancy test for calculating bias-corrected sex-chromosome
copy numbers.
Version: 1.4.4 [2010-02-08]
o Added appendVarArgs(boxplot.stats) so that one can pass argument
'show.names' to bxp() via plotRle().
Version: 1.4.3 [2010-02-03]
o Package passes R CMD check and all redundancy tests.
Version: 1.4.2 [2010-02-02]
o Updated to work with R.filesets v0.7.4 and aroma.core v1.4.4.
Version: 1.4.1 [2010-01-06]
o Now all binary files allocated have default NA values. This is done
by an update in aroma.core v1.4.1.
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Updated to aroma.core
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Version: 1.5.0 [2010-02-22]
o Submitted to CRAN. No changes since v1.4.7.
o Package passes R CMD check on R v2.10.1 patch and R v2.11.0 devel.
o Package passes all redundancy tests.
Version: 1.4.7 [2010-02-21]
o Added the AromaCellCpgFile class.
o Added Rd help for AromaCellPositionFile class.
Version: 1.4.6 [2010-02-19]
o SIMPLIFICATION: Now it is possible to use ChromosomeExplorer without
having to install the GLAD package (used before for cytobands).
o SIMPLIFICATION: Now it is possible to plot cytobands without having
to install the GLAD package.
o Argument 'zooms' of ChromosomeExplorer now default to 2^(0:6),
instead of 2^(0:7), because the images for zoom 2^7=128 would not
display in Firefox for the largest chromosomes.
o Updated getGenomeFile() for ChromosomalModel such that it can be used
to locate other types of genome annotation files as well, files that
may be optional (without giving an error).
o Added Human cytoband files to annotationData/genomes/.
o Added annotationData/genomes/ to aroma.core (from aroma.affymetrix).
o Added getOutputSet() for ChromosomalModel.
o Added alpha version of a doCBS().
Version: 1.4.5 [2010-02-10]
o ROBUSTNESS: Now also patches for R.filesets and R.utils are loaded,
if available, when aroma.core is loaded.
o CLEANUP: Removed debug print() statements in isCompatibleWith().
Version: 1.4.4 [2010-02-03]
o ROBUSTNESS: Package now requires matrixStats v0.1.9 or newer,
due to a bug in the earlier versions that would affect smoothing
of chromosomal signals that contains missing values.
o Package passes R CMD check and all redundancy tests.
Version: 1.4.3 [2010-01-25]
o ROBUSTNESS: Added a sanity check getChromosomes() for class
AromaUnitChromosomeTabularBinaryFile validating that the file
has a 'chromosome' column.
o CLEANUP: Using new Arguments$getTags() where ever possible.
Version: 1.4.2 [2010-01-13]
o ChromosomalModel:s (and and the ChromosomeExplorer) no
longer require unit names files.
o getListOfAromaUgpFiles() for ChromosomalModel no longer goes via
getListOfUnitNamesFiles(). This opens up the possibility to work
with data files without unit names files, e.g. smoothed CN data.
o Added getAromaUgpFile() for AromaPlatformInterface.
o Now getUnitNamesFile() for AromaPlatformInterface utilizes the
generic getUnitAnnotationDataFile() method.
Version: 1.4.1 [2010-01-06]
o Added argument 'defaults' to allocate() of AromaTabularBinaryFile.
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Updated to R.filesets
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Version: 0.8.0 [2010-02-22]
o Submitted to CRAN. No changes since v0.7.6.
Version: 0.7.6 [2010-02-13]
o Added argument '.onUnknownArgs' to GenericDataFile() and
GenericDataFileSet(). As before, the default is to throw an
exception if there are unknown arguments. However, in certain
case it is useful to allow (and ignore) "stray" arguments.
Version: 0.7.5 [2010-02-07]
o BUG FIX: indexOf() of GenericDataFileSet and GenericDataFileSetList
did not handle names with regular expression symbols '+' and '*'.
Thanks to Randy Gobbel for the initial error report.
Version: 0.7.4 [2010-01-31]
o DOCUMENATION: Added Rd help paged to more methods for classes
GenericDataFile and GenericDataFileSet.
o DEPRECATION: Deprecated static fromFiles() of GenericDataSet.
Use byPath() instead.
Version: 0.7.3 [2010-01-24]
o ROBUSTNESS: If argument 'files' is logical, then extract() of
GenericDataFileSet and GenericDataFileSetList now asserts that the
length of 'files' matches the number of available files.
Version: 0.7.2 [2010-01-12]
o Added some example data files under exData/.
o BUG FIX: readColumns(..., column=<string>) on a TabularTextFile
would give "Error ... object 'columnNames' not found".
Version: 0.7.1 [2010-01-02]
o Now setExtensionPattern(..., pattern=NULL) of GenericDataFile works.
o Added argument 'default="\\.([^.]+)$"' to getExtensionPattern()
of GenericDataFile. Before the default value was hardcoded
inside this function.
--
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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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