NEWS

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NormalyzerDE 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

NormalyzerDE 1.13.2

• Fixed leastRepCount setting of zero for statistics report

NormalyzerDE 1.9.1

• Version sync with Bioconductor

NormalyzerDE 1.5.5

• Updating the maintainer email

NormalyzerDE 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

NormalyzerDE 1.5.2

• Updated to follow Bioconductor release cycle
• Updated to fix issues in vignette introduced by updated external packages

NormalyzerDE 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.

NormalyzerDE 1.3.3

• Extended input validation when executing NormalyzerDE using experimentObj

NormalyzerDE 1.3.2

• Correctly showing the number of values replaced with NA in status text

NormalyzerDE 1.3.0

• Sync with Bioconductor changes

NormalyzerDE 1.1.16

• Clearer input verification error for both incorrect fields and when values < 1 are encountered

NormalyzerDE 1.1.14

• Updating tests to avoid cyclic dependency on the NormalyzerDE package

NormalyzerDE 1.1.13

• Running in reduced mode for small datasets (to avoid crashing on for instance VSN normalization and instead omitting it)

NormalyzerDE 1.1.12

• Pairwise Venn-diagrams in place

NormalyzerDE 1.1.11

• Fix minor issue where fully empty rows were filtered before substituting 'null' and '0' with NA

NormalyzerDE 1.1.10

• Add PCA visualizations showing which samples are included in each performed contrast

NormalyzerDE 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

NormalyzerDE 1.1.7

• Single-replicate runs fixed so that they run through correctly

NormalyzerDE 1.1.6

• Add support for assigning custom thresholds for statistics report

NormalyzerDE 1.1.5

• Issue corrected where pattern matching for zeroToNA option incorrectly was matching non-zero values.

NormalyzerDE 1.1.4

• Allow processing of non log-transformed data

NormalyzerDE 1.1.3

• Additional plots for statistical comparisons, and updated look

NormalyzerDE 0.99.24

• Various input checks added

NormalyzerDE 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

NormalyzerDE 0.99.21

• Documentation example fixes

NormalyzerDE 0.99.20

• Reactivate quantile normalization

NormalyzerDE 0.99.19

• Empty annotation no longer leads to crash when writing output

NormalyzerDE 0.99.17

• Very minor fix where function wasn't retrieved properly from SummarizedExperiment

NormalyzerDE 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

NormalyzerDE 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