Hi,
aroma.affymetrix v2.5.0 and friends have been updated. Update by running:
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.affymetrix");
The main update in this release is on the ArrayExplorer v3.4 and
ChromosomeExplorer v3.4, which can now be viewed (both locally and
online) with most modern web browsers including Firefox, Chrome,
Safari, Internet Explorer, and Opera. Thanks to Keith Ching and
Laurent Malvert for your help and comments making this possible.
Online examples can be seen at:
http://www.aroma-project.org/demos/
As usual there were also a few bug fixes and updates making the
pipelines more robust against mistakes. All details are below.
Enjoy,
Henrik
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Updates to aroma.affymetrix
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Version: 2.5.0 [2012-03-25]
o Submitted to CRAN.
o The package passes all redundancy tests.
Version: 2.4.3 [2012-03-23]
o CRAN POLICY: Package no longer utilizes .Internal() calls.
o CLEANUP: Deprecated PdInfo2Cdf() in favor (identical) pdInfo2Cdf(),
because the former does not follow the Aroma naming conventions.
Version: 2.4.2 [2012-03-06]
o GENERALIZATION: The new ArrayExplorer v3.4 will work with most
commonly used web browsers including Mozilla Firefox, Google Chrome,
Microsoft Internet Explorer, Apple Safari, and Opera.
o CRAN POLICY: Started to remove .Internal() calls.
Version: 2.4.1 [2012-01-14]
o ROBUSTNESS: Now the fit function of MbeiPlm gives an error
whenever one tries to use prior parameters, which are yet
not supported.
o Updated getFitUnitGroupFunction() for RmaPlm to support prior
probe-affinity parameters.
o Added argument 'listOfPriors' to MultiArrayUnitModel(). Such
priors are passed to the internal fitUnit() method.
o Now validate() of MultiArrayUnitModel accepts single-array data
sets, iff priors are set.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Updates to aroma.core
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
Version: 2.5.0 [2012-03-25]
o Submitted to CRAN.
o The package passes all redundancy tests.
Version: 2.4.13 [2012-03-23]
o Added alpha versions of PairedPSCNData and NonPairedPSCNData,
which inherits from RawGenomicSignals.
o Turned weightedMad() into a default method, added help documentation
with example code.
o CLEANUP: Moved (internal) swapXY() and draw() for 'density'
objects to R.utils (>= 1.10.0).
o BUG FIX: "["() for RichDataFrame would loose the class attribute,
unless argument 'drop' was FALSE.
Version: 2.4.12 [2012-03-15]
o Now colBinnedSmoothing(), colKernelSmoothing() and
colGaussianSmoothing() returns a matrix with column names
as in argument 'Y'.
o For RawGenomicSignals, added argument 'fields' to binnedSmoothing()
and binnedSmoothingByField(). Also added argument 'field' to
getSignals() and estimateStandardDeviation().
o Now RawGenomicSignals extends new internal RichDataFrame class.
o CLEANUP: Dropped deprecated files from the reports/includes/js/
directory installed by ArrayExplorer and ChromosomeExplorer.
Version: 2.4.11 [2012-03-12]
o Added binnedSmoothingByField() for RawGenomicSignals.
o Added subset() for RawGenomicSignals.
o Added get- and setVirtualField() for RawGenomicSignals.
o Added argument 'sort' to as.data.frame() for RawGenomicSignals.
Version: 2.4.10 [2012-03-06]
o GENERALIZATION: The new ArrayExplorer v3.4 will work with most
commonly used web browsers including Mozilla Firefox, Google Chrome,
Microsoft Internet Explorer, Apple Safari, and Opera.
Version: 2.4.9 [2012-03-06]
o ROBUSTNESS: Now all writeDataFrame() methods will add quotation
marks around column names that contain a comment character ('#').
This will make the written file readable with read.table() even
when there are header comments with prefix '#'. This issue was
reported by Yu Song at Oakland University.
o Now createImage() for matrix creates images of type "png::array"
by default (used to be "EBImage::Image"). If the latter, then
at least EBImage v3.9.7 (July 2011) is required.
o BUG FIX: write() for RasterImage would write truncated intensities,
because we forgot to rescale [0,65535] to [0,1] intensities.
Version: 2.4.8 [2012-03-02]
o GENERALIZATION: Now RawGenomicSignals inherits from data.frame
instead of Object. It works with the big aroma.affymetrix test
suite as well as with the TCGA vignette (of aroma.cn.eval).
Version: 2.4.7 [2012-03-01]
o Preparing for RawGenomicSignals not being reference variables.
o Preparing for supporting multiple-chromosome RawGenomicSignals.
o ROBUSTNESS: Added system tests for RawGenomicSignals classes.
o CLEANUP: Now R CMD check no longer reports that the package
is using .Internal() function calls. This was due to how we
adjusted colSums() and colMeans() to become generic functions.
Version: 2.4.6 [2012-02-04]
o Created ChromosomeExplorer v3.4, which should work on even more
browsers.
o GENERALIZATION: Now binnedSmoothing() of RawGenomicSignals default to
generate the same target bins as binnedSmoothing() of a numeric vector.
Before the bins had to be specified explicitly by the caller.
o GENERALIZATION: Now it is possible to call colBinnedSmoothing() with
an empty set of input loci, but still requesting a set of output loci,
which then will be all missing values.
o BUG FIX: Argument 'x' of colBinnedSmoothing() would default to the
incorrect number of loci.
Version: 2.4.5 [2012-02-03]
o GENERALIZATION: As ChromosomeExplorer v3.3, the new ArrayExplorer v3.3
works with most common web browsers. See below. However, we still
have problems getting ArrayExplorer to load the main spatial (PNG)
image in Internet Explorer.
o Forgot to include require.js in v2.4.4, which is needed by the
ChromosomeExplorer v3.3.
Version: 2.4.4 [2012-02-01]
o GENERALIZATION: The new ChromosomeExplorer v3.3 will work with most
commonly used web browsers including Mozilla Firefox, Google Chrome,
Microsoft Internet Explorer, Apple Safari and Opera. This far it has
been tested with the following browsers: Firefox v3.6/v9.01/v10.0,
Chrome v17.0, IE v7.x/v9.0, and Safari 5.
NOTE: To update an existing ChromosomeExplorer report, call
setup(ce, force=TRUE) where 'ce' is your ChromosomeExplorer object.
Thanks to Keith Ching at ConsultChing for the initial troubleshooting
[http://consultching.com/root/?p=64] leading me on the right track
on how update ChromosomeExplorer.
Version: 2.4.3 [2012-01-17]
o ROBUSTNESS: Now findPngDevice() tries all the available settings for
argument "type" of png(), for the current platform. This will
increase the chances for finding a PNG device that really works.
o SPEEDUP: Now findPngDevice() memoizes the results throughout the
current session.
o CLEANUP: Now findPngDevice() uses isPackageInstalled("Cairo") instead
of require("Cairo") to avoid loading Cairo if not really used.
Version: 2.4.2 [2012-01-14]
o BUG FIX: drawCytoband() for ChromosomalModel failed to locate the
genome annotation data file containing cytoband information, e.g.
Human,cytobands,<tags>.txt. Thanks to Kai Wang at Pfizer for
reporting on this.
o Added tag 'hg17' to Human,cytobands,hg17,GLADv2.4.0,HB20100219.txt
in annotationData/genomes/Human/.
Version: 2.4.1 [2012-01-12]
o CLEANUP: Dropped internal patch of base::serialize(), because it
was only applied to R (< 2.12.0) anyway and this package now
requires R (>= 2.12.0).
--
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/.
To post to this group, send email to [email protected]
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
