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NEWS
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NEWS
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CHANGES IN VERSION 1.5.1
-------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o
BUG FIXES AND MINOR IMPROVEMENTS
o simplified normalizeDat function, since array data and count data are treated the same, if repNormFactor (normalization factors) isn't provided by the user, then 75th percentile normalization is used. 10^6 multiplier that was used for per million read scaling is removed for the case of user provided repNormFactor (it's unlikely that this was used by most users)
o removed deprecated calls from ggplot2 (show_guide --> show.legend)
CHANGES IN VERSION 1.3.5
-------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Updated help files
BUG FIXES AND MINOR IMPROVEMENTS
o add warning if sample1Name or sample2Name include spaces or special characters.
CHANGES IN VERSION 1.3.4
-------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o None
BUG FIXES AND MINOR IMPROVEMENTS
o Fixed allReps and labelReps value assignment
o Fixed bug for duplicate row names in array data
o Fixed warning for incorrect sample names
CHANGES IN VERSION 1.3.3
-------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Updated dynRangePlot - function can now plot all replicates with or
without replicate labels
BUG FIXES AND MINOR IMPROVEMENTS
o Added warnings to initDat function for incorrect sample names and missing
1:1 controls from userMixFileß
o Set minimum version requirements for ggplot2 and gridExtra
CHANGES IN VERSION 1.3.2
-------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Vignette is updated to include use of grid.arrange for viewing figures
o multiplot function is deprecated and removed from the package,
function is replaced with grid.arrange
BUG FIXES AND MINOR IMPROVEMENTS
o updated erccROC, estLODR, and maSignal to address changes to tableGrob in
gridExtra package
CHANGES IN VERSION 1.3.1
-------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Version incremented to 1.3.1 for development.
BUG FIXES AND MINOR IMPROVEMENTS
o Updated DESCRIPTION file, NEWS file and .gitignore file
CHANGES IN VERSION 1.1.1
-------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Version incremented to 1.1.0 for Bioconductor 3.1 release.
BUG FIXES AND MINOR IMPROVEMENTS
o Updated NEWS file, DESCRIPTION file,and improved documentation in vignette.
CHANGES IN VERSION 1.0.0
-------------------------
SIGNIFICANT USER-VISIBLE CHANGES
o Version set to 1.0.0 for Bioconductor 3.0 release.
o No updates from 0.99.4.
CHANGES IN VERSION 0.99.4
-------------------------
BUG FIXES AND MINOR IMPROVEMENTS
o Updated saveERCCPlots, description file, and citation file.
CHANGES IN VERSION 0.99.1
-------------------------
BUG FIXES AND MINOR IMPROVEMENTS
o Fixed bug in erccROC and estLODR code to only use P-values from ERCCs by coding
"ERCC-00" prefix instead of "ERCC-" which in some cases might find endogenous
transcripts named with this prefix.
CHANGES IN VERSION 0.99.0
-------------------------
NEW FEATURES
o Version set to 0.99.0 for submission to Bioconductor
ISSUES
o CMD check still takes too long (> 5 minutes), probably due to differential
expression testing in underlying package. This will be difficult to change.
CHANGES IN VERSION 0.9.12
-------------------------
BUG FIXES AND MINOR IMPROVEMENTS
o Shortened vignette to reduce installation time
o Fixed userMixFile as.factor bug
o Updated namespace to pull in mgcv and nlme package functionality
ISSUES
o CMD check still takes too long (> 5 minutes), probably due to differential
expression testing in underlying package. This will be difficult to change.
CHANGES IN VERSION 0.9.11
-------------------------
BUG FIXES AND MINOR IMPROVEMENTS
o Added examples to several functions including "dontrun" to minimize
installation time
o Updated Namespace to include gplots