CHANGES IN VERSION 1.19.7 ---------------------------------- * Remove RCmdrMisc as dependency, resolving a fatal crash caused by updated signature of RCmdrMisc CV calculation function * Updating code to remove deprecation warnings for ggplot2 code CHANGES IN VERSION 1.13.2 ---------------------------------- * Fixed leastRepCount setting of zero for statistics report CHANGES IN VERSION 1.9.1 ---------------------------------- * Version sync with Bioconductor CHANGES IN VERSION 1.5.5 ---------------------------------- * Updating the maintainer email CHANGES IN VERSION 1.5.4 ---------------------------------- * Option to write output as PNG files * Option to use Limma trend=TRUE for including the intensity in its prior * State the design groups on second page in the NormalyzerDE report CHANGES IN VERSION 1.5.2 ---------------------------------- * Updated to follow Bioconductor release cycle * Updated to fix issues in vignette introduced by updated external packages CHANGES IN VERSION 1.3.4 ---------------------------------- * Certain datasets with fixed imputed values caused large difference in CV and MAD for RLR normalization, which in turn lead to a crash in the plotting functions. This update makes sure that the plotting can be carried out despite extreme values. CHANGES IN VERSION 1.3.3 ---------------------------------- * Extended input validation when executing NormalyzerDE using experimentObj CHANGES IN VERSION 1.3.2 ---------------------------------- * Correctly showing the number of values replaced with NA in status text CHANGES IN VERSION 1.3.0 ---------------------------------- * Sync with Bioconductor changes CHANGES IN VERSION 1.1.16 ---------------------------------- * Clearer input verification error for both incorrect fields and when values < 1 are encountered CHANGES IN VERSION 1.1.14/15 ---------------------------------- * Updating tests to avoid cyclic dependency on the NormalyzerDE package CHANGES IN VERSION 1.1.13 ---------------------------------- * Running in reduced mode for small datasets (to avoid crashing on for instance VSN normalization and instead omitting it) CHANGES IN VERSION 1.1.12 ---------------------------------- * Pairwise Venn-diagrams in place CHANGES IN VERSION 1.1.11 ---------------------------------- * Fix minor issue where fully empty rows were filtered before substituting 'null' and '0' with NA CHANGES IN VERSION 1.1.10 ---------------------------------- * Add PCA visualizations showing which samples are included in each performed contrast CHANGES IN VERSION 1.1.9 ---------------------------------- * Extensive testing suite set up * Bug fixes: - Technical replicates run through properly (previously crashed) - Using log-transformed input for normalization debugged * Refactor of statistics module to separate contrast filtering from object CHANGES IN VERSION 1.1.7 ---------------------------------- * Single-replicate runs fixed so that they run through correctly CHANGES IN VERSION 1.1.6 ---------------------------------- * Add support for assigning custom thresholds for statistics report CHANGES IN VERSION 1.1.5 ---------------------------------- * Issue corrected where pattern matching for zeroToNA option incorrectly was matching non-zero values. CHANGES IN VERSION 1.1.4 ---------------------------------- * Allow processing of non log-transformed data CHANGES IN VERSION 1.1.3 ---------------------------------- * Additional plots for statistical comparisons, and updated look CHANGES IN VERSION 0.99.24 ---------------------------------- * Various input checks added CHANGES IN VERSION 0.99.22 ---------------------------------- * Input parsing corrected so that a clear error message is provided when the design matrix samples doesn't match the data matrix header CHANGES IN VERSION 0.99.21 ---------------------------------- * Documentation example fixes CHANGES IN VERSION 0.99.20 ---------------------------------- * Reactivate quantile normalization CHANGES IN VERSION 0.99.19 ---------------------------------- * Empty annotation no longer leads to crash when writing output CHANGES IN VERSION 0.99.17/0.99.18 ---------------------------------- * Very minor fix where function wasn't retrieved properly from SummarizedExperiment CHANGES IN VERSION 0.99.16 ---------------------------------- * Crash when feeding SummarizedExperiment as input is fixed * If full rows contains only NA values they are filtered and a warning is generated CHANGES IN VERSION 0.99.15 ---------------------------------- * Corrected expected output from vapply in correlation matrix (where previous varying lengths caused crash) * Clearer error message when providing invalid sample/group conditions to statistics module * Issue where several identical RT-values caused crash in RT-slicing fixed