NEWS

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EDASeq 2.23.1

• Removed coercion methods to 'CountDataSet' following 'DESeq' deprecation.
• Updated vignette to show how to use 'EDASeq' with 'DESeq2'.

EDASeq 2.3

• Added function getGeneLengthAndGCContent to compute gene length and GC-content.
• Updated vignette.

EDASeq 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.

EDASeq 2.0

• "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.

EDASeq 1.9

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

EDASeq 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.

EDASeq 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.

EDASeq 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

EDASeq 0.99.0

• Version number changed for submission to Bioconductor

EDASeq 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

EDASeq 0.0.5

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

EDASeq 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

EDASeq 0.0.3

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