Changes in version 1.3: o Bugfix to the vignette; the two-panel (color) plot on page 6 used CQN corrected data as blue points in both panels. Now the left plot shows standard RPKM in blue. Thanks to Maria Keays . o Small fix to the vignette in the edgeR example, caused by changes to edgeR. o Updated the citations in the vignette and the CITATION file. o cqn.fixedlength has been removed, using cqn(lengthMethod = "fixed") instead. o A call slot has been added to cqn objects. o cqn() now accepts count matrices with 1 column or vectors (although it makes little sense to use the function on such data). o Added Questions and Answers to the vignette and moved vignette to vignettes dir. Changes in version 1.1: o Same fixes as in 1.0.1 o Resaved the data files, so they take up less space. o Added edgeR as a Suggests: since the vignette uses it. Changes in version 1.0.1: o The function alpha has been moved from ggplot2 to the new package scales. Vignette and Suggests: fields have been changed accordingly. o sizeFactors = NULL should now work for cqn and cq.fixedlength. Thanks to Maria Chikina for reporting this Changes in version 0.99: o Version bump as well as added to Bioconductor devel branch. o Wrote vignette. o Added additional manpages as well as examples. o Added data from Montgomery et al. o Added NAMESPACE file. o Added manpage for cqn. o Renamed cqn, cqn2. o Added NEWS.Rd file. o Added vignette skeleton. o Added CITATION file.