CHANGES IN VERSION 1.33.1 ------------------------- SIGNIFICANT USER-VISIBLE CHANGES / BUG FIX o Vignette output showed incorrect mRNA fraction estimates and incorrect LODR estimates due to the stringsAsFactors=FALSE switch with R > 4.0. Ratio values were not being treated as factors in the loadERCCInfo function and this was causing incorrect ratio value assignments in the est_r_m.R function. The issue has been resolved by an explicit as.factor assignment in the loadERCCInfo.R function. CHANGES IN VERSION 1.13.1 ------------------------- SIGNIFICANT USER-VISIBLE CHANGES o replaced QuasiSeq with edgeR for differential expression testing, due to deprecation of QuasiSeq o users will observe significant speed increases for DE testing o users will observe changes in results from example data, Quasi-Likelihood methods are similar for edgeR and QuasiSeq, but not exactly identical, so P-value distributions are different, LODR estimates have changed. o dispersion plot (dispPlot) is now generated via edgeR instead of QuasiSeq, using a similar Quasi-Likelihood dispersion shrinkage method. BUG FIXES AND MINOR IMPROVEMENTS o changed behavior so that dispPlot is not deleted if DE testing is rerun, instead increment file name to prevent overwriting. CHANGES IN VERSION 1.7.2 ------------------------- SIGNIFICANT USER-VISIBLE CHANGES o BUG FIXES AND MINOR IMPROVEMENTS o Fixed minor syntax issues in Rd files o Added more importFrom calls to Namespace file CHANGES IN VERSION 1.7.1 ------------------------- SIGNIFICANT USER-VISIBLE CHANGES o BUG FIXES AND MINOR IMPROVEMENTS o Fixed conditional statement for normalized microarray data in testDEArray. o Added dev.off to close the last plot in an attempt to prevent Rplots.pdf when run via Rscripts on commandline. 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