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NEWS
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NEWS
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CHANGES IN VERSION 1.23.2
----------------------------------
* Fix bug where non-categorical ANOVA setting wasn't applied
CHANGES IN VERSION 1.23.1
----------------------------------
* Remove unnecessary dependency (Biobase) by calling rowMedians with matrixStats::rowMedians instead
* Fix deprecation warning by using guide = "none" instead of FALSE
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