Hi,
aroma.affymetrix v2.13.0 and friends has been released and is now
available on CRAN for all the major operating systems. Intall/update
by:
source("http://callr.org/install#aroma.affymetrix";)
This will take care of all dependencies and recommended packages as
well (also those hosted on Bioconductor and elsewhere). BTW, you can
use this one-line approach to also install any CRAN and Bioconductor
packages out there.
What's new?
* Subsetting data sets and files is made more similar to how you work
with lists, e.g. ds[idxs] and ds[[idx]] works as expected. You can
safely stop using getFile(ds, idx) and use ds[[idx]] instead.
* `justRMA()` for AffymetrixCelSet replicates affx::justRMA(), but
does so with using much less memory allowing you to run 1000's of
arrays.
* As usal, bug fixes and robustness improvements (== you spend less
time troubleshooting and more time doing science). Although I keep
saying it, there's always ongoing work under the hood toward an
automagic parallel/distributed processing. It will happen one day.
Cheers,
Henrik
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Updates to aroma.affymetrix
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Version: 2.13.0 [2015-01-17]
o Bumped version for CRAN submission.
o Updated package dependencies.
o Package passes all redundancy tests.
Version: 2.12.10 [2015-01-06]
o CLEANUP: Major cleanup of namespace imports from suggested packages
such as affxparser and aroma.light.
Version: 2.12.9 [2014-11-17]
o Updated redundancy tests under testScripts/ to find rowMedians() of
the matrixStats package. The matrixStats package used to be attached
whenever aroma.light (< 2.1.1) was attached, but no longer.
Version: 2.12.8 [2014-09-04]
o ROBUSTNESS/BUG FIX: createFrom(..., mode="copy") for AffymetrixCelFile
would give an error on "No permission to modify existing file: ..."
iff the source file had read-only permission. This bug was introduced
by changes to base::file.copy() in R (>= 2.13.0) [April 2011].
Thanks to Taylor Raborn at Indiana University for reporting on this.
Version: 2.12.7 [2014-08-27]
o ROBUSTNESS: Added forgotten NAMESPACE imports.
Version: 2.12.6 [2014-06-29]
o BUG FIX: getAromaCellSequenceFile() for AffymetrixCdfFile used
undefined variable 'nbrOfCells'.
Version: 2.12.5 [2014-06-24]
o Added package system tests utilizing example data of Bioconductor
package AffymetrixDataTestFiles, iff installed.
Version: 2.12.4 [2014-06-09]
o Package now requires R (>= 3.0.0) and BioC (>= 2.13), which were
released April 2013 and are in fact old and it's recommended to
use a more recent version of R.
o Added 'SuggestsNote' field to DESCRIPTION with list of packages
that are recommended for the most common use cases.
o Bumped package dependencies.
Version: 2.12.3 [2014-05-02]
o CLEANUP: Now using ds[[idx]] instead of getFile(ds, idx) where possible.
Version: 2.12.2 [2014-04-28]
o Added justRMA() for AffymetrixCelSet, which with good precision
reproduces the results of the default setting of justRMA() in the
affy package. It does so by still running with a constant memory
profile. This means that a much larger number of samples can be
processed using this implementation.
o doCRMAv2(..., drop=FALSE) and hence doASCRMAv2(..., drop=FALSE), did
not *return* the base-position normalization step, although it was
done and its outcome was part of all downstream steps.
o extractExpressionSet() for ChipEffectSet gained argument 'orderUnitsBy'
and returns standard errors as well.
Version: 2.12.1 [2014-04-26]
o SPEEDUP: Minor speedup by replacing repetive <ns>::<fcn>() calls
with repetive <fcn>() calls; the '::' operator is fairly expensive.
You should expect a small speed improvement when using MatSmoothing(),
RmaPlm(..., flavor="oligo") and when calculating weights using
ExonRmaPlm and QualityAssessmentModel, to name a few examples.
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Updates to aroma.core
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Version: 2.13.0 [2015-01-07]
o Bumped version for CRAN submission.
o Updated package dependencies.
o Package passes all redundancy tests.
Version: 2.12.8 [2014-09-19]
o BUG FIX: display() for Explorer would try to open a pathname
in a way that only worked on Windows. Thanks to Sunghee Oh
(S. Korea) for reporting on this.
Version: 2.12.7 [2014-09-04]
o ROBUSTNESS: Wherever needed, files are now copied without preserving
file permissions (e.g. read-only), which became the default in
R (>= 2.13.0) [April 2013].
o Bumped package dependencies.
Version: 2.12.6 [2014-08-27]
o Now 'aromaSettings' are loaded when the packages is loaded.
Previously the package had to be attached.
o ROBUSTNESS: Now fit2d() for matrix utilizes use() for aroma.light.
o ROBUSTNESS: Added several missing NAMESPACE imports.
o BUG FIX: writeDataFrame(..., columnNamesPrefix="none") for
AromaUnitSignalBinaryFile would give an error.
Version: 2.12.5 [2014-06-28]
o Added getAromaUflFile() for AromaPlatformInterface.
o CLEANUP: Move byChipType() from classes AromaCellCpgFile and
AromaCellPositionFile to superclass AromaCellTabularBinaryFile.
o CLEANUP: Dropped getAromaUgpFile() for AromaUnitSignalBinaryFile.
o CLEANUP: Package does less package reordering.
o BUG FIX: SampleAnnotationSet$loadAll() would give an error if
annotationData/samples/ didn't exist or did not contain any SAF
files.
Version: 2.12.4 [2014-06-09]
o Package now requires R (>= 3.0.0) and BioC (>= 2.13), which were
released April 2013 and are in fact old and it's recommended to
use a more recent version of R.
o Added 'SuggestsNote' field to DESCRIPTION with list of packages
that are recommended for the most common use cases.
o Bumped package dependencies.
Version: 2.12.3 [2014-05-02]
o CLEANUP: Now using ds[[idx]] instead of getFile(ds, idx) where possible.
Version: 2.12.2 [2014-04-26]
o SPEEDUP: Minor speedup by replacing repetive <ns>::<fcn>() calls
with repetive <fcn>() calls; the '::' operator is fairly expensive.
Version: 2.12.1 [2014-03-04]
o CRAN POLICY: Now limiting the number of registered S3 methods in
NAMESPACE for R (< 3.1.0). Used to be R (< 3.0.2).
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Updates to R.filesets
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Version: 2.6.0 [2014-08-26]
o Added support for sortBy(..., by="filesize") and
sortBy(..., decreasing=TRUE) for GenericDataFileSet.
o Added rep() for GenericDataFileSet.
o Submitted to CRAN.
Version: 2.5.10 [2014-08-25]
o BUG FIX: readDataFrame() would ignore argument 'colClasses'
iff it had no names. Added package system test for this case.
Version: 2.5.9 [2014-08-23]
o BUG FIX: Using commentChar=NULL for TabularTextFile:s failed.
Version: 2.5.8 [2014-08-19]
o Added readChecksums() for ChecksumFileSet.
Version: 2.5.7 [2014-08-17]
o BUG FIX: byPath() for GenericDataFileSet would output verbose message
enumerating files loaded to stdout instead of stderr.
Version: 2.5.6 [2014-08-07]
o BUG FIX: dsApply() for GenericDataFileSet would coerce argument
'verbose' to logical before applying the function.
Version: 2.5.5 [2014-08-02]
o BUG FIX: Argument 'sep' for readDataFrame() would only work for
',' and '\t'; now it works for any separator.
o Bumped package dependencies.
Version: 2.5.4 [2014-06-11]
o Now indexOf() first searched by exact names, then as before, i.e.
by regular expression and fixed pattern matching. Added package
system tests that contains particularly complicated cases for this.
This was triggered by a rare but real use case causing an error in
aroma.affymetrix. Thanks Benilton Carvalho for reporting on this.
o Added argument 'by' to indexOf() for GenericDataFileSet|List.
Version: 2.5.3 [2014-06-07]
o Added 'SuggestsNote' field to DESCRIPTION with list of packages
that are recommended for the most common use cases.
o Bumped package dependencies.
Version: 2.5.2 [2014-05-02]
o CLEANUP: Now using ds[[idx]] instead of getFile(ds, idx) where possible.
Version: 2.5.1 [2014-04-19]
o dsApply(..., .parallel="none") would lower the verbose threshold
before applying the function resulting is less verbose output
in the non-parallel case.
--
--
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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