Hi,
I'm pleased to announce that we are now leaving the community of
v0.x.x projects - aroma.affymetrix v1.0.0 has been release (details at
the end). It is 3 years (and 2 days) to date since the project was
started. Since then a lot of new methods and features have been added
and more families of chip types are now supported. We can analyze
classical expression arrays, exon arrays, SNP & CN arrays, and tiling
arrays and resequencing arrays are around the corner. We can do all
this on Unix, Linux, Windows, and Mac OSX systems even with 1-1.5GB of
RAM. You can install the new version by:
source("http://www.braju.com/R/hbLite.R";);
hbInstall("aroma.affymetrix");
ACKNOWLEDGMENTS:
Since the start significant contributions to aroma.affymetrix have
been done by Ken Simpson, Elizabeth Purdom, and Mark Robinson, not to
mention the great work of James Bullard and Kasper Hansen for
developing affxparser (for reading/writing Affymetrix data files), as
well as Ben Bolstad for developing preprocessCore/affyPLM (for fitting
probe-level models and more). Important work has also been done by
Benilton Carvalho and Rafael Irizarry through their work on the oligo
package, which is becoming even more important now when we start
supporting CRLMM (genotyping) via aroma.affymetrix. Thanks also to
Benilton for giving tutorials on aroma.affymetrix. Pratyaksha (Asa)
Wirapati's has substantially contributed to the crosstalk-calibration
methods. Without these people, much of what is implemented would
still be on the drawing board. I also would also take the opportunity
to thank my postdoc adviser Terry Speed with collaborators for keep
pushing interesting projects that results in continuous development of
aroma.affymetrix. Thanks also to Affymetrix for their quick support
and feedback.
Alright, I haven't forgot about all others who contributed with
testing, troubleshooting and code patches: Pierre Neuvial (who we will
for sure hear more from), Lavinia Gordon, Jeremy Silver, Jason Li, Yue
Hu, Maria Traka, Maria Ortiz, Nicolas Stransky, Tim Keighley, Karen
Vranizan and many more (sorry if missed mention you by name). Thanks
also to everyone who helps answering questions on the mailing list -
most appreciated.
QUALITY:
Nope, I did not forget about all of you who are using the package -
there has been approximately 5-10 downloads per day the last year!
Anyone who use the package to analyze their own data are *truly*
contributing to the overall quality of the package. For every minute
and hours the package is used, the more likely it is that another bug
(they'll always be there) is spotted and reported. Please let these
reports keep coming (after making sure you use the latest version,
yada yada...). Success stories are of course also welcomed.
>From our side, we try to do the best to improve the quality of the
package. Before releasing a new version, the package must pass all
code tests of R CMD check flawlessly, and then it has to pass all
redundancy and replication tests on real data. The latter tests now
consist of more than 4,000 lines of code and takes approximately 15-20
hours to run on decent machines - you can find these tests in
system.file("testScripts", package="aroma.affymetrix"). Even when you
run the code yourself, continuous validation is applied throughout,
i.e. we assert the correctness of arguments and data, sanity of
estimates and results etc. Basically, we take the approach of not
trusting our own code (it now consists of more than 50,000 lines of
code) and tries to detect discrepancies as soon as they occur.
YOU CAN ALSO HELP:
Please note that this is an open source project, so any kind of
contributions are welcome. If you think you have a method for
aroma.affymetrix that would be helpful to others, please consider
sharing it. We also need help with documentation, examples, usecases,
vignettes, redundancy & replication tests, and help with building
annotation data files. If you have your own in-house tutorials,
please consider sharing it and we can either put it on the website
directly or link to it. Although we are all busy, please contact us
if you want to help out.
Looking forward to another great year!
Henrik
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UPDATES to aroma.affymetrix:
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Version: 1.0.0 [2009-01-12]
o Added alpha version of the CrlmmModel (currently only for 100K & 500K).
o Added justSNPRMA() replicating ditto in the oligo package.
o Added alpha version of the HaarSegModel.
o Added plotAllelePairs() for AllelicCrosstalkCalibration.
o Added argument 'zooms' to the constructor of ChromosomeExplorer.
o Now process() of AlleleSummation returns immediately if already done.
o Added more methods and classes which eventually will allow
analysis of Affymetrix tiling arrays.
o Added trial version of AromaCellPositionFile.
o Added extractCNT() and writeCNT() for SnpChipEffect{File|Set}, which
exports CNT data files that can be imported by Affymetrix GTC Browser.
o Added argument 'units' to readDataFrame() to GenomeInformation.
o ROBUSTNESS: Now MultiArrayUnitModel:s assert that there are at least
two arrays in the data set.
o BUG FIX: AlleleSummation would not work for chip types containing
exclusively SNP units. It expected some non-SNP units.
o CLEAN UP: createFrom() for AffymetrixCelFile had verbose=TRUE as default.
o BUG FIX: There was no extractTotalAndFreqB() for CnChipEffectSet,
but only for CnChipEffecSet (misspelled). Thanks Pierre Neuvial
for spotting this.
o BUG FIX: Now process() avoids sets of pairs with too few probe pairs.
This could happen because of the new getSetsOfProbes() working off
the probe sequence files.
o BUG FIX: getUnitIntensities() of AffymetrixCelSet would drop the array
dimension if only one array was read. This caused for instance PLM
fitting to given an error when only one array was included.
o BUG FIX: Methods returning ChipEffectSet would not "update" the
returned data set, which for instance had the effect of not
updating/setting attributes for sample annotation files.
o Lines of code (excluding comments) using grep -v "#" *.R | wc -l:
aroma.affymetrix + aroma.core: 43657+10510 = 54167.
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UPDATES to aroma.core:
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Version: 1.0.0 [2009-01-12]
o Added getMaxLengthRepeats() to AromaCellSequenceFile.
o Added AromaUnitSignalBinary{File|Set}, AromaUnitTotalCnBinary{File|Set},
AromaUnitFracBCnFinary{File|Set}, AromaUnitCall{File|Set}, and
AromaUnitGenotypeCall{File|Set}.
o BUG FIX: readFooter() of AromaTabularBinaryFile did not return the
correct list for nested structures.
o BUG FIX: groupBySnpNucleotides() of AromaCellSequenceFile would return
an empty element 'missing' for some chip types, e.g. Mapping10K_Xba142.
Now that empty elements are dropped.
o BUG FIX: getAttributes() for GenericDataFile:s would give an error
if there were no attributes.
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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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