CHANGES IN VERSION 1.39.5 ------------------------- o Depends on R > 4.0 o Converted from Sweave PDF vignette to Rmarkdown HTML. o Updating testDECount.R to handle changes made in edgeR o Updating saveERCCPlots.R to deal with grob error CHANGES IN VERSION 1.37.2 ------------------------- BUG FIXES AND MINOR IMPROVEMENTS o Added legacy=TRUE for glmQLFit() function from edgeR to maintain behavior equivalent to results with Bioconductor 3.16, rather than using the new method of adjustment for small counts from edgeR that was introduced in Bioconductor 3.18 (legacy = FALSE by default). Changes to the glmQLFit function in edgeR seem to be causing slight changes to dispersion results even with legacy=TRUE. 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