Hi,
aroma.affymetrix v2.7.0 is available. As usual, it is highly
recommended to update, which you can do by running:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
This release consists of several updates throughout the suite of
aroma.* and R.* packages. As always, all updates are backward
compatible, so all your scripts will work the same and you should get
identical results. The full list of updates (rather technical and
detailed) is below, but the quick summary is that:
o The package is getting more and more fault tolerant for every release.
o A few non-important bug fixes, i.e. nothing wrong was detected
forcing you to reanalyze anything.
o The interactive HTML reports ChromosomeExplorer and ArrayExplorer
[http://aroma-project.org/demos/] have been updated (to v3.5) and
should work in even more browsers. Thanks Laurent Malvert and others
at IDBS for helping out on this.
Enjoy,
Henrik
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Updates to aroma.affymetrix
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Version: 2.7.0 [2012-11-24]
o Bumped version for CRAN submission.
o Bumped up package dependencies.
o No updates.
o Package passes all redundancy tests.
Version: 2.6.16 [2012-11-21]
o Updated verbose output of parameters.
Version: 2.6.14 [2012-11-21]
o DOCUMENTATION: Hiding more internal methods from the help indices.
o CLEANUP: Now utilizing the new ParametersInterface.
o CLEANUP: Replaced all getParameterSet() with getParameters().
o CLEANUP: Deprecated "[" and "[[" for AffymetrixCelFile,
AffymetrixCelSet, CnagCfhFile, and CnagCfhSet.
o CLEANUP: bgAdjustOptical() and bgAdjustRma() for AffymetrixCelSet
are now defunct. Instead, see OpticalBackgroundCorrection and
RmaBackgroundCorrection.
o CLEANUP: bgAdjustGcrma() for AffymetrixCelSet no longer reads
and write probe affinity files in the deprecated APD format.
o CLEANUP: Removed obsolete code from internal bgAdjustOptical() that
was never reached and that loaded affinities via obsolete APD files.
Version: 2.6.13 [2012-11-18]
o Now package explicitly imports R.cache, because aroma.core is no
longer loading it.
Version: 2.6.12 [2012-11-14]
o CLEANUP: getWeights() for QualityAssessmentModel no longer sets the
alias of the returned data set, because the use of aliases is deprecated.
o CLEANUP: writeImage() for AffymetrixCelFile no longer supports
sample name aliases.
Version: 2.6.11 [2012-11-13]
o CLEANUP: Properly declared all cached fields, making it possible
to remove nearly all clearCache() implementations because the one
for Object takes does the job.
Version: 2.6.10 [2012-11-12]
o CLEANUP: Now seq_along(x) instead of seq(along=x) everywhere.
Similarly, seq(ds) where 'ds' is GenericDataFileSet is now
replaced by seq_along(ds). Likewise, seq_len(x) replaces
seq(length=x), and length(ds) replaces nbrOfFiles(ds).
Version: 2.6.9 [2012-11-08]
o Renamed getColumnNames() to getDefaultColumnNames() for all
classes inheriting from GenericTabularFile, because of the
new ColumnNamesInterface interface.
Version: 2.6.8 [2012-11-05]
o CLEANUP: Replaced all whichVector() with which(), because the
latter is now the fastest again.
Version: 2.6.7 [2012-10-29]
o CLEANUP: Now using Arguments$get(Read|Writ)ablePath() instead of
filePath(..., expandLinks="any").
Version: 2.6.6 [2012-10-21]
o ROBUSTNESS: Now using Arguments$getWritablePath() everywhere instead
of mkdirs(), because the former will do a better job in creating
and asserting directories on slow shared file systems, and when it
fails it gives a more informative error message.
Version: 2.6.5 [2012-10-18]
o ROBUSTNESS: Now createMonocellCdf() for AffymetrixCdfFile validates
the CDF (via new validate()). This will give more informative
error message in case the CDF is invalid, e.g. containing "empty"
units.
o ROBUSTNESS: Added validate() for AffymetrixCdfFile, which validate
a CDF for the most "common" errors, to help troubleshooting. Note
that the validation is not complete, i.e. rare/unknown errors are
not caught.
o Now as.character() for all AromaChipTypeAnnotationFile classes,
and hence print(), reports the file size both as abbreviated as
well as in exact number of bytes, e.g. "24.66 MB (25853850 bytes)"
(used to only be "24.66 MB").
Version: 2.6.4 [2012-10-16]
o ROBUSTNESS/BUG FIX: No longer passing '...' to NextMethod(), cf.
R-devel thread 'Do *not* pass '...' to NextMethod() - it'll do it
for you; missing documentation, a bug or just me?' on Oct 16, 2012.
Version: 2.6.3 [2012-10-14]
o CLEANUP: Moved AromaUnitGcContentFile to aroma.core.
o CLEANUP: Removed several defunct/obsolete methods and turned
deprecated methods into defunct/obsolete ones.
o CLEANUP: findByChipType() for AffymetrixCdfFile no longer support
monocell CDF file named <chipType>-monocell.CDF, and gives an
informative error if that is still the case. Since December 2007,
the filename should instead be <chipType>,monocell.CDF.
o CLEANUP: createParamCdf() for ChipEffectFile and FirmaFile no longer
support '<chipType>-monocell' filenames. If detected, an informative
error is thrown.
Version: 2.6.2 [2012-09-15]
o BUG FIX: doCRMAv2() failed to quickly located already available results
if the chip type of the CDF had tags, e.g. 'GenomeWideSNP_6,Full'.
Version: 2.6.1 [2012-09-14]
o BUG FIX/ROBUSTNESS: Although getUnitIntensities() for AffymetrixCelSet
would retrieve the CDF tree structure and pass it to affxparser's
readCelIntensities(), it was done in such a way that the latter would
still need to find and read the CDF. This meant that it would not
necessarily retrieve the same CDF as the AffymetrixCelSet used.
o MEMORY: Now getUnitIntensities() and readUnits() for AffymetrixCelSet
no longer cache the results in memory if argument 'units' is NULL.
o CLEANUP: Restructured part of the test scripts tree. Added a new
batch launcher.
o BUG FIX: The utility function for downloading individual CEL files
from GEO would give an error that it could not gunzip the downloaded
file, iff the filename extension was lower case, e.g. *.cel.gz
instead of *.CEL.gz.
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Updates to aroma.core
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Version: 2.7.1 [2012-11-26]
o Lowered the package dependencies to aroma.light (>= 1.22.0)
such that this package can be installed easily on R (>= 2.14.0).
o BUG FIX: getRam() and setRam() for AromaSettings did not use
'memory/ram'.
Version: 2.7.0 [2012-11-24]
o Bumped version for CRAN submission.
o Bumped up package dependencies.
o No updates.
o Package passes all redundancy tests.
Version: 2.6.16 [2012-11-21]
o Now getParametersAsString() handles sets of parameters as well.
o Added getParameterSets() to ParametersInterface.
Version: 2.6.15 [2012-11-21]
o Added ParametersInterface.
o DOCUMENTATION: Hiding more internal methods from the help indices.
Version: 2.6.14 [2012-11-18]
o CLEANUP: Dropped getHeaderParameters() for TextUnitNamesFile, which
is now done by getHeader() of TabularTextFile.
o CLEANUP: Now using getName() instead of deprecated getLabel().
o CLEANUP: Package only depends on digest indirectly via R.cache.
o CLEANUP: Moved internal .assertDigest() to R.cache.
Version: 2.6.13 [2012-11-13]
o CLEANUP: Properly declared all cached fields, making it possible
to remove nearly all clearCache() implementations because the one
for Object takes does the job.
o CLEANUP: The RSP template for ChromosomeExplorer's setupExplorer.js
had a duplicated entry.
Version: 2.6.12 [2012-11-12]
o CLEANUP: Now seq_along(x) instead of seq(along=x) everywhere.
Similarly, seq(ds) where 'ds' is GenericDataFileSet is now
replaced by seq_along(ds). Likewise, seq_len(x) replaces
seq(length=x), and length(ds) replaces nbrOfFiles(ds).
Version: 2.6.11 [2012-11-08]
o Renamed getColumnNames() to getDefaultColumnNames() for all
classes inheriting from GenericTabularFile, because of the
new ColumnNamesInterface interface.
o CRAN POLICY: Made a few of the examples faster. Also made
some of the system tests faster.
Version: 2.6.10 [2012-11-05]
o CLEANUP: Replaced all whichVector() with which(), because the
latter is now the fastest again.
Version: 2.6.9 [2012-10-31]
o Added argument 'units' to readDataFrame() for
AromaUnitChromosomeTabularBinaryFile.
Version: 2.6.8 [2012-10-29]
o CLEANUP: Now using Arguments$get(Read|Writ)ablePath() instead of
filePath(..., expandLinks="any").
Version: 2.6.7 [2012-10-21]
o Added argument 'maxNAFraction' to CopyNumberChromosomalModel, which
is now the prefer place to specify it, instead of to fit() etc.
o Now CopyNumberChromosomalModel() accepts references of type
"none", "constant(1)", "constant(2)", and "median", where "none"
and "constant(1)" are identical, "constant(2)" uses reference signals
that are exactly 2, and "median" uses reference signals are equals
the robust average across all samples. For backward compatibility,
NULL is still supported, which equals "median".
o ROBUSTNESS: Now using Arguments$getWritablePath() everywhere instead
of mkdirs(), because the former will do a better job in creating
and asserting directories on slow shared file systems, and when it
fails it gives a more informative error message.
o BUG FIX: Scrolling in the ChromosomeExplorer by dragging the
navigator bar was broken.
Version: 2.6.6 [2012-10-18]
o It is no longer possible to have different *versions* of ArrayExplorer
and ChromosomeExplorer under the same reports/ directory structure.
If you wish to keep old Explorer reports, rename those reports/
root directories.
o ROBUSTNESS/BUG FIX: Some of the HTML and CSS errors in ArrayExplorer
and ChromosomeExplorer that were detected by the W3's online validation
services were correct.
o BUG FIX: A few errors in the Javascript of ArrayExplorer has been
corrected. It also does a better job of inferring the height of the
displayed spatial image. Thanks Laurent Malvert (ID Business Solutions
Ltd; IDBS) for the report, troubleshooting and suggestions on this.
Version: 2.6.5 [2012-10-17]
o ROBUSTNESS: Now all static Object methods that calls "next" methods,
utilizes NextMethod(), which became possible with R.oo v1.10.0.
Version: 2.6.4 [2012-10-16]
o ROBUSTNESS/BUG FIX: No longer passing '...' to NextMethod(), cf.
R-devel thread 'Do *not* pass '...' to NextMethod() - it'll do it
for you; missing documentation, a bug or just me?' on Oct 16, 2012.
Version: 2.6.3 [2012-10-14]
o Added AromaUnitGcContentFile (from aroma.affymetrix).
o CLEANUP: Removed several defunct/obsolete methods and made
deprecated methods defunct/obsolete.
Version: 2.6.2 [2012-10-11]
o Now aroma.core imports R.methodsS3 and R.oo.
This solves issues such as trim() being overridden by ditto
from the IRanges package, iff loaded.
Version: 2.6.1 [2012-09-14]
o Added exportAromaUnitPscnBinarySet() for a list.
o BUG FIX: exportAromaUnitPscnBinarySet() for AromaUnitTotalCnBinarySet
would throw an error if the files of the exported data set was
ordered in a non-lexicographic order.
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Updates to R.filesets
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Version: 1.6.0 [2012-11-15]
o No updates. Bumped the version for CRAN release.
Version: 1.5.4 [2012-11-15]
o BACKWARD COMPATIBILITY: Made it possible for TabularTextFile to ignore
header comment arguments when inferring column names and classes.
Version: 1.5.3 [2012-11-13]
o CLEANUP: Now clearCache() for GenericDataFileSet relies on ditto
of Object to clear all cached fields (=with field modifier "cached").
o CLEANUP: Deprecated (get|set)Label() for GenericDataFile and
(get|set)Alias() for GenericData(File|FileSet). Related
arguments such at 'alias' to GenericDataFileSet and 'aliased'
to getDefaultFullName() for GenericDataFile are also deprecated.
Version: 1.5.2 [2012-11-12]
o CLEANUP: Now seq_along(x) instead of seq(along=x) everywhere.
Similarly, seq(ds) where 'ds' is GenericDataFileSet is now
replaced by seq_along(ds). Likewise, seq_len(x) replaces
seq(length=x), and length(ds) replaces nbrOfFiles(ds).
Version: 1.5.1 [2012-11-08]
o Now TabularTextFile() tries to infer whether the data section
contains column names or not. This is done by comparing to
the optional 'columnNames' header argument. If that is not
available, it will (as before) assume there are column names.
o Now readDataFrame() acknowledge header comment arguments
'columnNames' and 'columnClasses' if specified in the file.
o Now getDefaultColumnNames() for TabularTextFile falls back to
header comment argument 'columnNames', if there are no column
names in the actual data table.
o Now readRawHeader() for TabularTextFile also parses and returns
header comment arguments.
Version: 1.5.0 [2012-11-02]
o Added ColumnNamesInterface which GenericTabularFile now implements.
Classes inheriting from GenericTabularFile should rename any
getColumnNames() method to getDefaultColumnNames().
o CLEANUP: Replaced all whichVector() with which(), because the
latter is now the fastest again.
Version: 1.4.2 [2012-11-01]
o Added setColumnNames() for GenericTabularFile, which utilizes
setColumnNamesTranslator().
o CLEANUP: Deprecated (get|set)ColumnNameTranslator() in favor of
(get|set)ColumnNamesTranslator(); note the plural form.
Version: 1.4.1 [2012-10-31]
o CLEANUP: readDataFrame() for TabularTextFile no longer returns
attribute 'fileHeader', unless argument 'debug' is TRUE.
Version: 1.4.0 [2012-10-30]
o Added validate() to GenericDataFileSet, which iteratively calls
validate() on all the GenericDataFile:s in the set. The default
is to return NA, indicating that no validation was done.
Version: 1.3.3 [2012-10-29]
o CLEANUP: Now using Arguments$getReadablePath() instead of
filePath(..., expandLinks="any").
Version: 1.3.2 [2012-10-17]
o CLEANUP: Forgot to drop Arguments$getFilename() below.
Version: 1.3.1 [2012-10-16]
o ROBUSTNESS/BUG FIX: No longer passing '...' to NextMethod(), cf.
R-devel thread 'Do *not* pass '...' to NextMethod() - it'll do it
for you; missing documentation, a bug or just me?' on Oct 16, 2012.
Version: 1.3.0 [2012-10-16]
o CLEANUP: Moved Arguments$getFilename() from this package to
R.utils v1.17.0.
o ROBUSTNESS: Bumped up package dependencies.
Version: 1.2.2 [2012-10-16]
o DOCUMENTATION: Added Rd help for a few more methods.
o CLEANUP: static fromFiles() for GenericDataFileSet is now defunct
in placefor byName(), which has been recommended since January 2010.
Version: 1.2.1 [2012-09-27]
o Now readDataFrame() for TabularTextFile defaults to read strings
as characters rather than as factors. To read strings as factors,
just pass argument stringsAsFactors=TRUE.
o Added readDataFrame() for TabularTextFileSet.
o ROBUSTNESS: Now getHeader() for TabularTextFile checks if the
file has been modified before returned cached results.
Version: 1.2.0 [2012-09-25]
o Now R.filesets imports R.methodsS3, R.oo and R.utils.
This solves issues such as trim() being overridden by ditto
from the IRanges package, iff loaded.
Version: 1.1.6 [2012-09-01]
o CONSISTENCY: Now extractMatrix() for GenericTabularFile adds column
names just as ditto for GenericTabularFileSet does.
--
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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