THe output object from cqn() now has an additional component: glm.offset which is an offset matrix which can directly be used in a GLM type model (specifically edgeR). The usage is explained in the vignette secion on Import into edgeR. Previously the vignette recommended using the offset component of the cqn output, which is wrong, due to a scaling issue. The offset component of cqn is unchanged. This bug was found by Mike Love [email protected] and fixed in CQN 1.5.1.
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 [email protected].
Small fix to the vignette in the edgeR example, caused by changes to edgeR.
Updated the citations in the vignette and the CITATION file.
cqn.fixedlength has been removed, using cqn(lengthMethod = "fixed") instead.
A call slot has been added to cqn objects.
cqn() now accepts count matrices with 1 column or vectors (although it makes little sense to use the function on such data).
Added Questions and Answers to the vignette and moved vignette to vignettes dir.
Same fixes as in 1.0.1
Resaved the data files, so they take up less space.
Added edgeR as a Suggests: since the vignette uses it.
The function alpha has been moved from ggplot2 to the new package scales. Vignette and Suggests: fields have been changed accordingly.
sizeFactors = NULL should now work for cqn and cq.fixedlength. Thanks to Maria Chikina for reporting this
Version bump as well as added to Bioconductor devel branch.
Wrote vignette.
Added additional manpages as well as examples.
Added data from Montgomery et al.
Added NAMESPACE file.
Added manpage for cqn.
Renamed cqn, cqn2.
Added NEWS.Rd file.
Added vignette skeleton.
Added CITATION file.