Changes in version 3.12.0:

    o   read.maimages() with source="agilent" now reads median foreground
	estimates instead of mean foreground.  New option source=
	"agilent.mean" preserves earlier meaning of source="agilent".

    o   Agilent single-channel case study added to User's Guide.

    o   removeBatchEffect() now corrects for continuous covariates as well
	as qualitative factors.

    o   new function camera() performs competitive gene set tests while
	adjusting for inter-gene correlation.

    o   new function interGeneCorrelation() estimates the average intergene
	correlation for a set of genes.

    o   columns in output from roast() have been re-ordered.

    o   arguments 'selected' and 'selected2' renamed to 'index' and
	'index2' in functions barcodeplot(), geneSetTest() and wilcoxGST().

    o   default labels for barcodeplot() are now somewhat more explicit.

    o   new function rankSumTestWithCorrelation extends the
	Wilcoxon-Mann-Whitney test to allow for correlation between cases
	in one of the groups.  geneSetTest() now calls this function
	instead of wilcox.test, with a consequence improvement in speed.

    o   The lfc (log-fold-change) cutoff argument of topTable() is now
	applied to the minimum absolute logFC when ranking by F-statistic.
	Previously lfc was only used when ranking by t-statistic.

    o   new methods "fast" and "affy" for normalizeCyclicLoess(), with
	"fast" becoming the default method. New argument 'cyclic.method'
	for normalizeBetweenArrays() gives access to the different cyclic
	loess methods.

    o   There were problems with using the argument gene.weights in
	mroast().  This argument is now permitted to be of the same length
	as the number of probes in the data set.  It is then automatically
	subsetted for each gene set.

    o   mroast() now uses mid-p-values by default when adjusting for
	multiple testing.

    o   neqc(), nec() and normexp.fit.control() now give user-friendly
	error messages when no negative control probes or no regular probes
	are found.

Changes in version 3.10.0:

    o   New function voom() allows RNA-Seq experiments to be analysed using
	the standard limma pipeline. An RNA-Seq case study is added to
	User's Guide.

    o   treat(), roast() and mroast() can now estimate and work with a
	trend on the prior variance, bringing them into line with eBayes().

    o   barcodeplot() and barcodeplot2() merged into one function.

    o   removeBatchEffect() can now correct for two batch factors.

    o   plotMDS is now an S3 generic function.  This allows MDS plots to be
	redrawn with new labels without needing to repeat the distance or
	scaling calculations. New S4 class "MDS" to hold the
	multidimensional scaling information output from plotMDS.

    o   getEAWP() now gets probe annotation from the expression rownames of
	an EList object, if no other probe annotation is available.

    o   topRomer() now ranks gene sets by secondary columns as well the
	primary criterion specified, to give a more meaningful ranking when
	the p-values are tied.

    o   wilcoxGST() now accepts signed or unsigned test statistics. Change
	to p-value calculation in geneSetTest() when rank.only=FALSE to
	avoid zero p-values and follow recommendation of Phipson and Smyth
	(SAGMB, 2010).

    o   plotMA() now recognizes ElistRaw and EList objects appropriately.

    o   Default span for normalizeCyclicLoess increased from 0.4 to 0.7.
	Speed improved when weights=NULL.

    o   Weaver case study (Section 11.5) in User's Guide is updated and
	rewritten. Data classes ElistRaw and Elist now described in the
	quick start section of the User's Guide.  Other minor updates to
	User's Guide.

    o   Bug fix for normalizeBetweenArrays() when object is an EListRaw and
	method="cyclicloess".  Previously this function was applying
	cyclicloess to the raw intensities, then logging.  Now it logs
	first, then applies cyclicloess.

    o   Bug fix to avereps() for EList objects x when x$other is not empty.