Changes in version 1.29.2 o Update maintainer list, adding Måns Zamore as an author Changes in version 1.23.2 o Fix bug where non-categorical ANOVA setting wasn't applied Changes in version 1.23.1 o Remove unnecessary dependency (Biobase) by calling rowMedians with matrixStats::rowMedians instead o Fix deprecation warning by using guide = "none" instead of FALSE Changes in version 1.19.7 o Remove RCmdrMisc as dependency, resolving a fatal crash caused by updated signature of RCmdrMisc CV calculation function o Updating code to remove deprecation warnings for ggplot2 code Changes in version 1.13.2 o Fixed leastRepCount setting of zero for statistics report Changes in version 1.9.1 o Version sync with Bioconductor Changes in version 1.5.5 o Updating the maintainer email Changes in version 1.5.4 o Option to write output as PNG files o Option to use Limma trend=TRUE for including the intensity in its prior o State the design groups on second page in the NormalyzerDE report Changes in version 1.5.2 o Updated to follow Bioconductor release cycle o Updated to fix issues in vignette introduced by updated external packages Changes in version 1.3.4 o 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 o Extended input validation when executing NormalyzerDE using experimentObj Changes in version 1.3.2 o Correctly showing the number of values replaced with NA in status text Changes in version 1.3.0 o Sync with Bioconductor changes Changes in version 1.1.16 o Clearer input verification error for both incorrect fields and when values < 1 are encountered Changes in version 1.1.14 o Updating tests to avoid cyclic dependency on the NormalyzerDE package Changes in version 1.1.13 o 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 o Pairwise Venn-diagrams in place Changes in version 1.1.11 o Fix minor issue where fully empty rows were filtered before substituting 'null' and '0' with NA Changes in version 1.1.10 o Add PCA visualizations showing which samples are included in each performed contrast Changes in version 1.1.9 o Extensive testing suite set up o Bug fixes: - Technical replicates run through properly (previously crashed) - Using log-transformed input for normalization debugged o Refactor of statistics module to separate contrast filtering from object Changes in version 1.1.7 o Single-replicate runs fixed so that they run through correctly Changes in version 1.1.6 o Add support for assigning custom thresholds for statistics report Changes in version 1.1.5 o Issue corrected where pattern matching for zeroToNA option incorrectly was matching non-zero values. Changes in version 1.1.4 o Allow processing of non log-transformed data Changes in version 1.1.3 o Additional plots for statistical comparisons, and updated look Changes in version 0.99.24 o Various input checks added Changes in version 0.99.22 o 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 o Documentation example fixes Changes in version 0.99.20 o Reactivate quantile normalization Changes in version 0.99.19 o Empty annotation no longer leads to crash when writing output Changes in version 0.99.17 o Very minor fix where function wasn't retrieved properly from SummarizedExperiment Changes in version 0.99.16 o Crash when feeding SummarizedExperiment as input is fixed o If full rows contains only NA values they are filtered and a warning is generated Changes in version 0.99.15 o Corrected expected output from vapply in correlation matrix (where previous varying lengths caused crash) o Clearer error message when providing invalid sample/group conditions to statistics module o Issue where several identical RT-values caused crash in RT-slicing fixed