Changes in Version 2.1
----------------------

* Fixed bug in plotPCA: parameter k was not passed properly in SeqExpressionSet method.
* Fixed bug in plotQuality: trimming when reads of different lengths in same BAM/FASTQ files.

Changes in Version 2.0 (Major update)
----------------------

* "exprs" and "exprs<-" are now deprecated: use "counts" and "counts<-" instead (for compatibility with the DESeq class).
* "counts" now accesses the original counts (even after normalization) and "normCounts" accesses the normalized counts.
* Added the slot "normalizedCounts" to the SeqExpressionSet class: now the normalization functions will save the normalized counts in this new slot while keeping the original counts in "counts."
* Added option to "MDPlot" to visualize control genes in red.
* withinLaneNormalization and betweenLaneNormalization now always store the normalized counts in the normalizedCounts slot, even when offset=TRUE is used.
* Added a new method plotPCA for Principal Components Analysis (PCA) plots.
* Updated the vignette to reflect these changes.
* DESCRIPTION and NAMESPACE cleaned up.

Changes in Version 1.9
-----------------------

* Added method plotRLE for Relative Log Expression (RLE) plots.

Changes in Version 1.3
------------------------

* Fixed a bug in biasPlot relative to the lwd, xlab and ylab arguments.
* Added a color_code option and changed the behavior of col in biasPlot.
* Updated CITATION file.
* Added an option to withinLaneNormalization and betweenLaneNormalization to return unrounded values.
* A new way to deal with zero counts by adding a small positive constant.

Changes in Version 1.2
------------------------

* Fixed a bug in methods plotQuality and plotNtFrequency that now allow the strand information to be missing in the SAM/BAM file.
* Fixed a bug in method biasPlot. It doesn't require anymore that one of the column of pData is called "conditions".
* biasPlot method of SeqExpressionSet has now the argument "col" to specify the column of pData to use for color coding.

Changes in Version 0.99.1
------------------------

* The read-level EDA is now based on the classes BamFileList and FastqFileList of Rsamtools. The class ShortReadSet doesn't exist anymore.
* Changed vignette

Changes in Version 0.99.0
------------------------

* Version number changed for submission to Bioconductor

Changes in Version 0.0.6
------------------------

* Fixed a bug in withinLaneNormalization to work with unnamed matrices
* Fixed a bug in biasPlot to work with a single lane experiment
* Added methods MDPlot and biasBoxplot
* Changed the vignette and added an help page for newSeqExpression function

Changes in Version 0.0.5
------------------------

* Modified coerce from SeqExpressionSet to CountDataSet to treat the two class comparison in a separate way

Changes in Version 0.0.4
------------------------

* Added Vignette
* Adjusted xlab in the boxplot method for signature FastqQuality
* Changed getOffset and setOffset<- methods in offst and offst<- for compatibility with edgeR

Changes in Version 0.0.3
------------------------

* Added CITATION file
* Added Help pages
* Added data and extdata for the examples
