Changes in version 1.4.1:

    o   BUGFIX: Fixed format of NEWS.Rd, added reference to additional
	vignette in companion package gCMAPWeb.

Changes in version 1.3.5:

    o   NEW: DESeq package is now listed as 'Suggested' instead of
	'Depends'

Changes in version 1.3.4:

    o   NEW: Removed lattice and reshape dependencies.

    o   NEW: Removed cmapQAPlot function.

    o   NEW: Added generate_gCMAP_NChannelSet's 'report.center' parameter.

Changes in version 1.3.3:

    o   NEW: Experimented with cmapQAPlot function (removed again in
	version 1.3.4).

Changes in version 1.3.2:

    o   NEW: New mgsa_score method wrapping the model-based gene set
	analysis approach available in the mgsa package.

Changes in version 1.3.1:

    o   NEW: New KEGG2cmap, reactome2cmap, wiki2cmap and go2cmap to
	functions to generate CMAPCollections from public annotation
	databases

    o   NEW: New upIds and downIds methods for CMAPCollection objects.

Changes in version 1.3.0:

    o   NEW: fisher_score method now accepts NChannelSets as 'sets' and
	thresholds a channel of choice on the fly.

    o   BUGFIX: induceCMAPCollection method was updated to fix a bug that
	prevented processing of certain single-sample eSets.

    o   NEW: New parameters 'center.z' and 'center.log_fc' for the
	generate_gCMAP_NChannelSet function, centering each column of the
	score matrix on the column mean, median or density peak.
	(Internally, the new 'center_eSet' function is called.)

    o   NEW: New function 'center_eSet' to center columns of eSet channels
	on either their kernel density peak, their mean or their median.

    o   NEW: New function mergeCMAPs to combined two eSets that share
	class, varLabels, annotation and assayDataElementNames.

    o   BUGFIX: Fixed missing gene names in featureScores method with
	CMAPCollections queries containing single-gene sets.

    o   NEW: New splitPerturbations function to split ExpressionSet (e.g.
	downloaded from ArrayExpress) by annotations provided in the
	phenoData slot.

    o   NEW: New eset_instances function to generate lists eSets from
	larger datasets by specifying an instance.matrix.

    o   NEW: New setSizes methods for CMAPCollections returns a data.frame
	with the number of members for each gene set stored in the
	Collection.

    o   NEW: fisher_score method now reports z-scores in the effect column
	instead of log-odds-ratio. The latter are returned in the new,
	separate LOR column.

    o   NEW: featureScores method now return list of matched identfiers
	when dispatched on two CMAPCollection.

    o   NEW: Added 'density.only', 'level.only' and 'strip.only' parameters
	to the CMAPResults plot method to selectively return only one plot
	component.

    o   IMPROVED: Reduced memory footprint of gsealm_jg_score and
	induceCMAPCollection methods.

    o   CHANGED: By default, 'removeShift' option for gsealm_jg_score and
	gsealm_score methods is now set to FALSE.

    o   BUGFIX: Corrected sign of effect size for fisher_score for perfect
	overlap between set and query.

    o   IMPROVED: Improved plot method for CMAPResults objects, lattice
	package is no longer required.

Changes in version 1.1.4:

    o   BUGFIX: The gealm_score method is not defined for queries with
	missing values and will now return the corresponding error message.
	\itmeBUGFIX: GeneSetCollections containing only one set are
	processed correctly by gsealm_score.

Changes in version 1.1.3:

    o   BUGFIX: Corrected sign of effect size for fisher_score for perfect
	overlap between set and query.

Changes in version 1.1.2:

    o   BUGFIX: Fixed log-odds calculation in fisher_score: non-overlapping
	sets now get a log odds ratio of 0

Changes in version 1.1.1:

    o   IMPROVED: Reduced memory footprint of induceCMAPCollection method
	for bigmemory-backed eSet objects.

Changes in version 1.1.0:

    o   NEW: Version number was increased for the Bioconductor release.

Changes in version 0.99.6:

    o   IMPROVED: Updated mapIdentifiers method for SignedGeneSet class now
	handles more different annotation types.

Changes in version 0.99.5:

    o   NEW: The BigMatrix package changed its name to bigmemoryExtras.
	Currently, bigmemoryExtras only supports Mac and Unix platforms,
	thus gCMAP does not support Windows, either.

Changes in version 0.99.1:

    o   NEW: First release of the gCMAP package to Bioconductor.