NEWS

---

ribiosExpression 1.3.5

Bioconductor preparation

• Added biocViews to DESCRIPTION.
• Added BiocStyle vignette.
• Updated R dependency to >= 4.4.0.
• Added @return tags to all exported functions.
• Fixed typos in documentation.
• Replaced class(x) %in% with is.numeric().
• Converted NEWS to NEWS.md format.

ribiosExpression 1.0-39

• parseDesignContrast adds new parameter expSampleNames to allow sample name consistency check with input matrix.

ribiosExpression 1.0-34

• DesignContrast prints error message if validity is violated.
• parseDesignContrastFile fixes a mistake of assigning group levels.
• parseDesignContrastFile now accepts the dispLevelStr option.

ribiosExpression 1.0-33

• parseDesignContrastStr fixes two errors.

ribiosExpression 1.0-32

• Add DesignContrast object.

ribiosExpression 1.0-29

• Add new functionality in keepMaxMeanProbes.Rscript: able to read from .CHIP file.
• keepMaxMeanProbes.Rscript now does not depend on the S4 class ExpressionSet anymore, therefore much faster.

ribiosExpression 1.0-28

• Debug keepMaxMeanProbes.Rscript: extname returns NA if not found, therefore an additional check is added.

ribiosExpression 1.0-27

• Function extension in ChipFetcher2ExpressionSet: now non-Affymetrix probesets are supported as well.

ribiosExpression 1.0-26

• The main body of readCls has been moved to ribiosIO::read_cls. readCls becomes a synonym for compatibility.

ribiosExpression 1.0-25

• Improvement in readCls: error messages provide more informative details for mal-formatted files.

ribiosExpression 1.0-24

• Bug fix in writeEset: expression matrix is written without quotes.
• New script: keepMaxMeanProbes.Rscript filters duplicated genes by taking the one with maximum average expression.

ribiosExpression 1.0-23

• Bug fix in readGct: if input feature names have duplicates, the exprs matrix row names are changed.

ribiosExpression 1.0-22

• Move exprsMat2gct.Rscript to the ribiosIO package.
• writeGct has been refactored for matrix in ribiosIO, and re-implemented as an S4-method for matrix and ExpressionSet.

ribiosExpression 1.0-21

• Add exprsMat2gct.Rscript to convert between expression matrix files and GCT files.

ribiosExpression 1.0-20

• ChipFetcher2ExpressionSet: add option orthologue.
• keepMaxStatProbe uses function(x) mean(x, na.rm=TRUE) as default function.

ribiosExpression 1.0-19

• limma2gsea.Rscript is updated.

ribiosExpression 1.0-18

• Refactor GSEA-related functions that are not dependent on the Biobase data structure to the ribiosGSEA package.

ribiosExpression 1.0-17

• limma2gsea.Rscript guarantees no replicated gene symbols after orthologue mapping.

ribiosExpression 1.0-16

• Add limma2gsea.Rscript to inst/Rscript.

ribiosExpression 1.0-15

• The ribiosAnnotation package has been removed from the dependency list.
• Add comp_diff.Rscript to inst/Rscript.

ribiosExpression 1.0-14

• The deprecation message of remainHighestVarProbe and keepHighestVarProbe have been updated.

ribiosExpression 1.0-13

• The rowscale method warns if the input ExpressionSet does not have 'lockedEnvironment' as storageMode.

ribiosExpression 1.0-12

• Low-level functions for computational drug repositioning refactored into ribiosReposition.

ribiosExpression 1.0-11

• Add feature in summarizeProbesets: option keep.featureNames.
• Rename and rewrite sprintGmt to formatGmt as S4 method.

ribiosExpression 1.0-10

• Bugfix in readEset for numeric column names.
• Add annotate and reannotate methods.
• Add documentation for the ribios.ExpressionSet object.

ribiosExpression 1.0-9

• Add kendallW function and kendallWmat S4-method.

ribiosExpression 1.0-8

• PCA-related data structures and functions are refactored into the ribiosPCA package.

ribiosExpression 1.0-7

• Add summarizeProbesets to summarize probesets.
• NAMESPACE are now explicitly stated.

ribiosExpression 1.0-6

• Add dependency on the ribiosAnnotation package.
• Add writeEset and readEset functions.
• readFKdata was renamed as readFKtable.

ribiosExpression 1.0-5

• Add git version control.

ribiosExpression 1.0-4

• Move data.frame and matrix functions to the ribiosUtils package.

ribiosExpression 1.0-3

• Refactor read_gct into ribiosIO for efficiency.

ribiosExpression 1.0-2

• Change keepHighestVarProbe to more generalized keepMaxStatProbe.

ribiosExpression 1.0-1

• Remove the path option from the readGctCls function.