Changes in version 3.31.1 (2023-06-30) Documentation - Update redirecting and broken URLs. - Fix R CMD check notes on "Escaped LaTeX specials: &". Changes in version 3.31.0 (2023-04-25) Notes - The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.18 for R (>= 4.4.0). Changes in version 3.30.0 (2023-04-25) Notes - The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.17 for R (>= 4.3.0). Changes in version 3.29.0 (2022-11-01) Changes in version 3.28.0 (2022-11-01) Changes in version 3.27.0 (2022-04-26) - The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.16 for R-devel. Changes in version 3.26.0 (2022-04-26) - The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.15 for R (>= 4.2.0). Changes in version 3.25.1 (2022-04-21) Bug Fixes - Fixed partial argument name used in iwpca(). Changes in version 3.24.0 (2021-10-27) - The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.14 for R (>= 4.1.1). Changes in version 3.23.1 (2021-08-19) Documentation - Update several citation URLs that were either broken or redirects elsewhere. Changes in version 3.22.0 (2021-05-19) - The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.13 for R (>= 4.0.3). Changes in version 3.20.0 (2020-10-27) - The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.12 for R (>= 4.0.0). Changes in version 3.18.0 (2020-04-27) - The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.11 for R (>= 3.6.1). Changes in version 3.17.1 (2019-12-09) Code Refactoring - Now importing throw() from R.oo instead of R.methodsS3. Changes in version 3.17.0 (2019-10-30) - The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.11 for R (>= 3.6.1). Changes in version 3.16.0 (2019-10-30) - The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.10 for R (>= 3.6.1). Changes in version 3.15.1 (2019-08-28) Bug Fixes - wpca() for matrices had a length > 1 in coercion to logical bug. Changes in version 3.15.0 (2019-05-02) - The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.10 for R (>= 3.6.0). Changes in version 3.14.0 (2019-05-02) - The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.9 for R (>= 3.6.0). Changes in version 3.13.0 (2018-10-30) - The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.9 for R (>= 3.6.0). Changes in version 3.12.0 (2018-10-30) - The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.8 for R (>= 3.5.0). Changes in version 3.11.2 (2018-09-04) Code Refactoring - fitPrincipalCurve() now requires princurve (>= 2.1.2) and was updated to make use of new principcal_curve class instead of deprecated principcal.curve class. This update "should not" affect the results, but see https://github.com/rcannood/princurve/issues/8 for information of what has changed in the princurve package in this respect. Changes in version 3.11.1 (2018-08-28) - Updated installation instructions in README.md. Changes in version 3.11.0 (2018-04-30) - The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.8 for R (>= 3.6.0). Changes in version 3.10.0 (2018-04-30) - The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.7 for R (>= 3.5.0). Changes in version 3.9.1 (2017-12-19) New Features - robustSmoothSpline() now supports using Tukey's biweight (in addition to already exising L1) estimators. See argument method. Thanks to Aaron Lun at the Cancer Research UK Cambridge Institute for adding this feature. Changes in version 3.9.0 (2017-10-30) - The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.7 for R (>= 3.5.0). Changes in version 3.8.0 (2017-10-30) - The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.6 for R (>= 3.4.0). Changes in version 3.7.0 (2017-04-23) - The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.6 for R (>= 3.4.0). Changes in version 3.6.0 (2017-04-23) - The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.5 for R (>= 3.4.0). Changes in version 3.5.1 (2017-04-14) Significant Changes - robustSmoothSpline() uses a re-weighted re-iterative algorithm that fits a smooth spline using stats::smooth.spline(), calculates the residuals and which are used to fit a re-weighted smooth spline and so on until converence. Due to updates to stats::smooth.spline() in R (>= 3.4.0) it is no longer feasible to maintain a highly optimized version of the algorithm, because it was based on internal stats::smooth.spline() code that has no completely changed. Instead the re-iterative algorithm calls stats::smooth.spline() as is, which slows it down. More importantly, it will now give slightly different estimates. Software Quality - In addition to continous integration (CI) tests and nightly Bioconductor tests, the package is now also tested regularly against all reverse package depencies available on CRAN and Bioconductor. Changes in version 3.5.0 (2016-10-18) - The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.5 for R (>= 3.4.0). Changes in version 3.4.0 (2016-10-18) - The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.4 for R (>= 3.3.1). Changes in version 3.3.2 (2016-09-16) Code Refactoring - Using NA_real_ (not just NA) everywhere applicable. Bug Fixes - robustSmoothSpline() gave an error since R-devel (>= 3.4.0 r70682). Changes in version 3.3.1 (2016-08-10) Code Refactoring - CLEANUP: Using seq_len() and seq_along() everywhere (Issue #8) Changes in version 3.3.0 (2016-05-03) - The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.4 for R (>= 3.3.0). - The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.4 for R (>= 3.3.0). Changes in version 3.2.0 (2016-05-03) - The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.3 for R (>= 3.3.0). Changes in version 3.1.1 (2016-01-06) - Package requires R (>= 2.15.2). - CLEANUP: robustSmoothSpline() no longer generates messages that ".nknots.smspl() is now exported; use it instead of n.knots()" for R (>= 3.1.1). Changes in version 3.1.0 (2015-10-23) - The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.3 for R (>= 3.3.0). Changes in version 3.0.0 (2015-10-13) - The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.2 for R (>= 3.2.2). Changes in version 2.99.0 (2015-10-06) - No changes. Changes in version 2.9.0 (2015-09-17) Significant Changes - Argument preserveScale for normalizeTumorBoost() now defaults to FALSE. Since 1.33.3 (2014-04-30) it had no default and prior to that it was TRUE. Changes in version 2.5.3 (2015-09-13) Software Quality - ROBUSTNESS: Explicitly importing core R functions. Bug Fixes - rowAverages() and normalizeAverages() would give an error if some of the argument default functions are overridden by non-functions of the same name in the calling environment. Changes in version 2.5.2 (2015-06-16) Software Quality - Relaxed package test for backtransformPrincipalCurve(). Changes in version 2.5.1 (2015-05-24) - Bumped package dependencies. Deprecated and Defunct - Removed obsolete wpca(..., method = "dsvdc"); was only needed for backward compatibility with R (< 1.7.0). Changes in version 2.5.0 (2015-04-16) - The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.2 for R (>= 3.3.0). Changes in version 2.4.0 (2015-04-16) - The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.1 for R (>= 3.2.0). Changes in version 2.3.3 (2015-02-18) New Features - If a value of argument xlim or ylim for plotDensity() is NA, then it defaults to the corresponding extreme value of the data, e.g. plotDensity(x, xlim = c(0, NA)). Changes in version 2.3.2 (2015-02-17) Software Quality - ROBUSTNESS: Added package tests. Code coverage is 76%. Code Refactoring - CLEANUP: Using requestNamespace() instead of request(). Changes in version 2.3.1 (2014-12-08) - Same updates as in 2.2.1. Changes in version 2.3.0 (2014-10-13) - The version number was bumped for the Bioconductor devel version, which is now Bioconductor 3.1 for R (>= 3.2.0). Changes in version 2.2.1 (2014-12-08) Code Refactoring - Minor code cleanup. Changes in version 2.2.0 (2014-10-13) - The version number was bumped for the Bioconductor release version, which is now Bioconductor 3.0 for R (>= 3.1.1). Changes in version 2.1.2 (2014-09-23) - Minor tweaks due to the move to GitHub. Changes in version 2.1.1 (2014-09-16) Software Quality - Fixed some new R CMD check NOTEs. Code Refactoring - CLEANUP: Now importing R.utils (instead of only suggesting it). - IMPORTANT/CLEANUP: The matrixStats package is no longer attached with this package. In other words, you now might have to add library(matrixStats) to your scripts. Changes in version 2.1.0 (2014-04-11) - The version number was bumped for the Bioconductor devel version, which is now Bioconductor 2.15 for R (>= 3.1.0). Changes in version 2.0.0 (2014-04-11) - The version number was bumped for the Bioconductor release version, which is now Bioconductor 2.14 for R (>= 3.1.0). Changes in version 1.99.3 (2014-03-31) - Bumped the version such that the next release will be 2.0.0. Changes in version 1.33.3 (2014-03-30) Significant Changes - Argument preserveScale for normalizeTumorBoost() is now required. The goal with this is to in a future version migrate to use preserveScale = FALSE as the default (was preserveScale = TRUE) in order to avoid introducing a a global bias in the tumor allele B fraction of heterozygous SNPs. The examples use preserveScale = FALSE now. New Features - Added pairedAlleleSpecificCopyNumbers(). Changes in version 1.33.2 (2014-03-25) New Features - Now plotDensity() supports weights via argument W. Changes in version 1.33.1 (2014-03-25) New Features - Now plotDensity() also supports density() objects. Code Refactoring - CLEANUP: robustSmoothSpline() no longer uses DUP = FALSE in an internal .Fortran() call. - Bumped up package dependencies. Changes in version 1.33.0 (2013-10-14) - The version number was bumped for the Bioconductor devel version. Changes in version 1.32.0 (2012-10-14) - The version number was bumped for the Bioconductor release version, which is now Bioconductor 2.13 for R (>= 3.0.0). Changes in version 1.31.10 (2013-10-08) New Features - Added averageQuantile() for matrices in addition to lists. Performance - SPEEDUP: Now normalizeQuantileSpline(..., sortTarget = TRUE) sorts the target only once for lists of vectors just as done for matrices. Documentation - Merged the documentation for normalizeQuantileSpline() for all data types into one help page. Same for plotXYCurve(). Code Refactoring - Bumped up package dependencies. Bug Fixes - Argument lwd of plotXYCurve(X, ...) was ignored if X was a matrix. Changes in version 1.31.9 (2013-10-07) New Features - Now library(aroma.light, quietly = TRUE) attaches the package completely silently without any messages. - Now the aroma.light Package object is also available when the package is only loaded (but not attached). Documentation - Merged the documentation for normalizeQuantileRank() for numeric vectors and lists. - Now documention S3 methods under their corresponding generic function. Changes in version 1.31.8 (2013-10-02) Documentation - More generic functions are now "aliased" under relevant corresponding methods. Changes in version 1.31.7 (2013-09-27) Performance - SPEEDUP: Now all package functions utilizes matrixStats functions where possible, e.g. anyMissing(), colMins(), and rowWeightedMedians(). Code Refactoring - Bumped up package dependencies. Changes in version 1.31.6 (2013-09-25) Code Refactoring - CLEANUP: Package no longer use a fallback attachment of the R.oo package upon attachment. Changes in version 1.31.5 (2013-09-23) Software Quality - ROBUSTNESS: Now properly declaring all S3 methods in the NAMESPACE file. Performance - SPEEDUP/CLEANUP: normalizeTumorBoost() now uses which() instead of whichVector() of R.utils. Before R (< 2.11.0), which() used to be 10x slower than whichVector(), but now it's 3x faster. Code Refactoring - CLEANUP: Now only using Authors@R in DESCRIPTION, which is possible since R (>= 2.14.0). Hence the new requirement on the version of R. - Bumped up package dependencies. Changes in version 1.31.4 (2013-09-10) Software Quality - CLEANUP: Now package explicitly imports what it needs from matrixStats. Code Refactoring - Bumped up package dependencies. Changes in version 1.31.3 (2013-05-25) Performance - SPEEDUP: Removed all remaining gc() calls, which were in normalizeQuantileSpline(). - SPEEDUP: Replaced all rm() calls with NULL assignments. Code Refactoring - Updated the package dependencies. Changes in version 1.31.2 (2013-05-20) - Same updates as in v1.30.2. Changes in version 1.31.1 (2011-04-18) - Same updates as in v1.30.1. Changes in version 1.31.0 (2013-04-03) - The version number was bumped for the Bioconductor devel version. Changes in version 1.30.5 (2013-09-25) Software Quality - Backport from v1.31.5: Declaring all S3 methods in NAMESPACE. Code Refactoring - Backport from v1.31.5: normalizeTumorBoost() now uses which(), which also removes one dependency on R.utils. Changes in version 1.30.4 (2013-09-25) Software Quality - Backport from v1.31.4: Now package explicitly imports what it needs from matrixStats. Changes in version 1.30.3 (2013-09-25) Performance - Backport from v1.31.3: Removal of all gc() calls and removal of variables is now faster. Bug Fixes - Removed one stray str() debug output in robustSmoothSpline(). Changes in version 1.30.2 (2013-05-20) Changes in version 1.30.1 (2013-04-18) New Features - Now backtransformPrincipalCurve() preserves dimension names. Bug Fixes - backtransformPrincipalCurve() gave an error if the pricipal curve was fitted using data with missing values. - fitPrincipalCurve() would not preserve dimension names if data contain missing values. Changes in version 1.30.0 (2012-04-03) - The version number was bumped for the Bioconductor release version, which now is Bioconductor 2.12 for R (>= 3.0.0). Changes in version 1.29.0 (2012-10-01) - The version number was bumped for the Bioconductor devel version. Changes in version 1.28.0 (2012-10-01) - The version number was bumped for the Bioconductor release version, which now is Bioconductor 2.11 for R (>= 2.15.1). Changes in version 1.27.1 (2012-09-12) Software Quality - ROBUSTNESS: Replaced an .Internal(psort(...)) call in medianPolish() with a call to matrixStats:::.psortKM(). Changes in version 1.27.0 (2012-08-30) Code Refactoring - CLEANUP: Removed weightedMedian(), which has been moved to the matrixStats package. - BACKWARD COMPATIBILITY: Now package depends on the matrixStats (>= 0.5.2) package, so that weightedMedian() is still available when loading this package. In future releases, matrixStats will be downgraded to only be a suggested package. Changes in version 1.26.1 (2012-08-30) Code Refactoring - Updated the package dependencies. Bug Fixes - robustSmoothSpline() would not work with most recent R devel versions. Changes in version 1.26.0 (2012-08-19) Significant Changes - Changed the license of aroma.light to GPL (>= 2) from LGPL (>= 2), because some of the implementation was adopted from GPL (>= 2) code, i.e. robustSmoothSpline() uses code from stats::smooth.spline(). Software Quality - R CMD check no longer warns about some examples depending on the R.basic package. Changes in version 1.25.4 (2012-08-19) Software Quality - WORKAROUND: Now robustSmoothSpline() robustly locates the proper native R fit function for smooth splines, which vary with different releases of R. Changes in version 1.25.3 (2012-04-16) Code Refactoring - Package no longer depends on R.methodsS3, only imports. Changes in version 1.25.2 (2012-04-16) Software Quality - R CMD check no longer complaints about .Internal() calls. Changes in version 1.25.1 (2012-04-16) New Features - Added support for fitNaiveGenotypes(..., flavor = "fixed"). - GENERALIZATION: Now fitNaiveGenotypes() returns also flavor and tau. The latter are the genotype thresholds used by the caller. Code Refactoring - CLEANUP: Dropped argument flavor of callNaiveGenotypes(); it is instead passed to fitNaiveGenotypes() via .... Changes in version 1.25.0 (2012-03-30) - The version number was bumped for the Bioconductor devel version. Changes in version 1.24.0 (2012-03-30) - The version number was bumped for the Bioconductor release version, which now is Bioconductor 2.10 for R (>= 2.15.0). Changes in version 1.23.0 (2011-10-31) - The version number was bumped for the Bioconductor devel version. Changes in version 1.22.0 (2011-10-31) - The version number was bumped for the Bioconductor release version, which now is Bioconductor 2.9 for R (>= 2.14.0). Changes in version 1.21.2 (2011-10-10) Code Refactoring - Updated robustSmoothSpline() such that it works with the new "uniqueness" scheme of smooth.spline() in R v2.14.0 and newer. It is tricky, because robustSmoothSpline() is a reiterative algorithm which requires that the choosen "unique" x:s does not change in each iteration. Previously, signif(x, 6) was used to identify unique x:s, which gives the same set of values when called twice, whereas this is not true for the new choice with round((x - mean(x))/tol). Changes in version 1.21.1 (2011-06-26) New Features - Added argument aspectRatio to plotMvsA(). It can be used to adjust the range of the Mlim argument relative to the Alim argument. Changes in version 1.21.0 (2011-04-13) - The version number was bumped for the Bioconductor devel version. Changes in version 1.20.0 (2010-04-13) - The version number was bumped for the Bioconductor release version, which now is Bioconductor 2.8 for R (>= 2.13.0). Changes in version 1.19.6 (2011-04-12) Code Refactoring - CLEANUP: Removed internal patch of principal.curve(). If an older version than princurve v1.1-10 is used, an informative error is thrown requesting an update. The internal patch is part of the offical princurve v1.1-10 release (since 2009-10-04). - Now all methods allocate objects with NAs of the appropriate mode. Known Issues - Recent updates to smooth.spline() in R v2.14.0 causes robustSmoothSpline() to break in some cases. Changes in version 1.19.5 (2011-04-08) New Features - Now weightedMedian() returns NA:s of the same mode as argument x. Changes in version 1.19.4 (2011-03-03) Changes in version 1.19.3 (2011-02-05) Changes in version 1.19.2 (2010-10-22) Changes in version 1.19.1 (2010-10-18) Changes in version 1.19.0 (2010-10-18) - The version number was bumped for the Bioconductor devel version. Changes in version 1.18.4 (2011-03-03) Bug Fixes - findPeaksAndValleys(x, to) were x is numeric would use partial match and interpret to as argument tol and not part of ... passed to density(). This problem was solved by placing ... before argument tol. Thanks Oscar Rueda at the Cancer Reasearch UK for reporting on and identifying this bug. Changes in version 1.18.3 (2011-02-05) Documentation - Added paragraphs on how to do affine normalization when channel offsets are known/zero. Same for multiscan calibration when scanner offsets are known/zero. - Fixed broken links to help for iwpca(). Changes in version 1.18.2 (2010-10-22) Documentation - Minor clarifications to the help page on "1. Calibration and Normalization". This page is now also referenced in help("calibrateMultiscan"). Changes in version 1.18.1 (2010-10-18) New Features - Argument censorAt for fitNaiveGenotypes() has new default. - These updates were supposed to be in v1.17.7, but we forgot to commit them to the Bioconductor repository before the new Bioconductor release. Bug Fixes - fitNaiveGenotypes(..., subsetToFit = ) would throw an exception reporting Some elements of argument subsetToFit is out of range .... Changes in version 1.18.0 (2010-10-18) - The version number was bumped for the Bioconductor release version, which now is Bioconductor 2.7 for R (>= 2.12.0). Changes in version 1.17.6 (2010-10-08) New Features - Now findPeaksAndValleys() returns a object of class PeaksAndValleys, which extends data.frame. Changes in version 1.17.5 (2010-10-07) New Features - Added optional argument fit to callNaiveGenotypes() for passing a model fit returned by fitNaiveGenotypes(). If not specified, callNaiveGenotypes() will call fitNaiveGenotypes() internally. - Added fitNaiveGenotypes(), which previously was only internal of callNaiveGenotypes(). Changes in version 1.17.4 (2010-10-06) New Features - Added findPeaksAndValleys() for the density class, which then findPeaksAndValleys() for numeric utilizes. Changes in version 1.17.3 (2010-09-18) Software Quality - ROBUSTNESS: Now normalizeFragmentLength() asserts that arguments fragmentLengths and y contain at least some finite values and specifies the same number of units. In addition, the method also gives more informative error messages in case it cannot fit the normalization function due to non-finite values. Changes in version 1.17.2 (2010-08-04) New Features - Added argument preserveScale to normalizeTumorBoost() to rescale the calibrated allele B fractions for heterozygous SNPs such that the compression relative to the homozgygotes is preserved. Changes in version 1.17.1 (2010-07-23) Changes in version 1.17.0 (2010-04-22) - The version number was bumped for the Bioconductor devel version. Changes in version 1.16.1 (2010-07-23) New Features - Now callNaiveGenotypes() returns the model estimates as attribute modelFit. This feature was supposed to be in v1.16.0. Changes in version 1.16.0 (2010-04-22) - The version number was bumped for the Bioconductor release version, which now is Bioconductor 2.6 for R (>= 2.11.0). Changes in version 1.15.4 (2010-04-08) Software Quality - R devel assumes ASCII encoding unless specified. Added explicit Latin-1 encoding to the DESCRIPTION file to R CMD check to pass. Changes in version 1.15.3 (2010-04-04) New Features - Added normalizeDifferencesToAverage(), normalizeTumorBoost(), callNaiveGenotypes() and internal findPeaksAndValleys(), which all were moved from the aroma.cn package. Changes in version 1.15.2 (2010-03-12) Bug Fixes - The example of fitPrincipalCurve() used a non-existing argument name in the calls to substitute(). Thanks to Brian Ripley at University of Oxford for reporting this. Changes in version 1.15.1 (2009-11-01) Code Refactoring - Now fitPrincipalCurve() only uses the internal bug-fix patch if a version earlier than princurve v1.1-10 is installed. Changes in version 1.15.0 (2009-10-27) - The version number was bumped for the Bioconductor devel version. Changes in version 1.14.0 (2009-10-27) - The version number was bumped for the Bioconductor release version, which now is Bioconductor 2.5 for R (>= 2.10.0). Changes in version 1.13.6 (2009-10-20) Documentation - FIX: CITATION file reverted to that of v1.13.4. Changes in version 1.13.5 (2009-10-08) Documentation - CITATION file (incorrectly) updated by Bioconductor maintainers. Changes in version 1.13.4 (2009-09-23) Documentation - Fixed a few broken Rd links. Changes in version 1.13.3 (2009-07-15) New Features - ADDED: fitXYCurve() and backtransformXYCurve(). - Added attribute processingTime to the fit object returned by fitPrincipalCurve(). Changes in version 1.13.2 (2009-05-29) Changes in version 1.13.1 (2009-05-13) Changes in version 1.13.0 (2009-04-20) Changes in version 1.12.2 (2009-05-29) Code Refactoring - Replacing old HOWTOCITE with a standard CITATION file. Bug Fixes - Previous bug fix in backtransformPrincipalCurve() regarding argument dimension broke the initial purpose of this argument. Since both use cases are still of interest, how the subsetting is done is now based on whether the number of dimensions of the input data and the model fit match or not. See help and example code for backtransformPrincipalCurve.matrix(). Changes in version 1.12.1 (2009-05-13) Bug Fixes - backtransformPrincipalCurve(..., dimensions) did not subset the X matrix. Also, the method now returns a matrix of the same number of columns requested. The Rd example now illustrates this. Thanks to Pierre Neuvial, UC Berkeley for the troublshooting and fix. Changes in version 1.12.0 (2009-04-20) - The version number was bumped for the Bioconductor release version. Changes in version 1.11.2 (2009-02-08) Bug Fixes - An error was thrown in backtransformPrincipalCurve() when argument dimensions was specified. Changes in version 1.11.1 (2009-01-12) New Features - Added fitPrincipalCurve() and backtransformPrincipalCurve(). Changes in version 1.11.0 (2008-10-21) - The version number was bumped for the Bioconductor devel version. Changes in version 1.10.0 (2008-10-21) - The version number was bumped for the Bioconductor release version. Changes in version 1.9.2 (2008-09-11) New Features - Added argument onMissing to normalizeFragmentLength() for specifying how to normalize, if at all, data points for which the fragment lengths are unknown. For backward compatibility, we start off by having it "ignore" by default. Code Refactoring - MEMORY OPTIMIZATION: robustSmoothSpline() is now cleaning out more variables when no longer needed. Changes in version 1.9.1 (2008-05-10) Changes in version 1.9.0 (2008-04-29) - The version number was bumped for the Bioconductor devel version. Changes in version 1.8.1 (2008-05-10) Bug Fixes - If the subsetToFit of normalizeFragmentLength() was shorter than the number of data points, an exception was thrown. The test was supposed to assert that the subset was not greater than the number of data points. Changes in version 1.8.0 (2008-04-29) - The version number was bumped for the Bioconductor release version. Changes in version 1.7.2 (2008-04-14) New Features - Added normalizeFragmentLength(). - Added normalizeQuantileSpline(). - Renamed normalizeQuantile() to normalizeQuantileRank(). - Added plotXYCurve(). - Added predict() for the lowess class. Changes in version 1.7.1 (2007-11-28) New Features - The startup message when loading the package is generated with packageStartupMessage() so that it can be suppressed. Documentation - TYPO: Corrected a spelling error in the help pages. Software Quality - Package passes R CMD check for R v2.6.1. Code Refactoring - Package now only suggest the R.oo package, and instead depends on the new R.methodsS3. Changes in version 1.7.0 (2007-10-08) - The version number was bumped for the Bioconductor devel version. Changes in version 1.6.0 (2007-10-08) - The version number was bumped for the Bioconductor release version. Changes in version 1.5.2 (2007-08-10) Software Quality - Package pass R CMD check for R v2.6.0. Changes in version 1.5.1 New Features - Added normalizeAverage(). Software Quality - Package pass R CMD check for R v2.6.0 with Rd encoding errors. Changes in version 1.5.0 (2007-05-09) - The version number was bumped for the Bioconductor devel version. Changes in version 1.4.0 (2007-05-09) - The version number was bumped up with the Bioconductor release. Changes in version 1.3.1 (2007-01-15) Code Refactoring - Removed code to use modreg for backward compatibility with R < 1.9.0. - Added R.utils to Suggests field of DESCRIPTION. Changes in version 1.3.0 (2006-10-03) - The devel version number was bumped up with the Bioconductor release. Changes in version 1.2.0 (2006-10-03) - The version number was bumped up with the Bioconductor release. Changes in version 1.1.0 (2006-07-20) Significant Changes - Added to Bioconductor 1.9. New Features - Added some trial RSP pages. Try browseRsp() in the R.rsp package. Changes in version 0.1.7 (2006-06-27) Code Refactoring - Made the package truely standalone except from R.oo. Previously package R.basic was used in some of the examples. Changes in version 0.1.6 (2006-05-22) New Features - Added medianPolish() which is much faster than stats::medpolish() when there are no NA. - Added plotDensity() for list of vectors as well as for matrices. - Added normalizeQuantile() for lists of vectors as well as for a single vector of numerics. To calculate the target quantile there is a new function averageQuantile(), which is also for lists of vectors. It latter does not support robust estimatation of the average, because it safes memory. - Updated normalizeQuantile() for matrices according to the updates in the limma package. Code Refactoring - Added a namespace for the package. - Added biocViews since the package will eventually be added to the Bioconductor project. Changes in version 0.1.5 (2006-04-21) Performance - Minor speedup to weightedMedian(), e.g. negative weights do no longer give and error, but are treated as zero instead. This removes some overhead of the function. Also, if it is known that there are no NAs that can be specified by na.rm = NA, which will skip NA checks. Changes in version 0.1.4 (2006-03-28) Documentation - Updated broken Rd links. - Updated the references to publications. Changes in version 0.1.3 (2006-01-22) New Features - Now fitIWPCA() does not return the data matrix. This is to save memory. The calling algorithm can equally well add the data if it is needed. Documentation - Added help on the returned parameters of fitIWPCA(). Changes in version 0.1.2 (2005-09-06) New Features - All plot methods displaying log-ratios now assures that no fake log-ratios are calculated due to two negative raw signals. Similarily, methods display log-intensities now assures that the log-intensities are calculated as doubles to avoid possible overflow warnings for too large integers. Changes in version 0.1.1 (2005-07-26) New Features - Added sampleCorrelations() and sampleTuples(). - Now argument interpolate of weightedMedian() defaults to TRUE only if ties is NULL. Changes in version 0.1.0 (2005-06-03) Significant Changes - Created. Most of the matrix methods were copied from the R.basic and the aroma packages. The purpose of this package is to provide a standalone package, which does not require any of the aroma classes. This will allow the methods to be used by end users as is, or be utilized in other packages.