edgeR
1 June 2009, edgeR 1.3.3
- paste() replaced with file.path() in vignette.
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add a few more checks to the DGEList constructor
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small modifications to 'exactTestNB' defaults
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Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
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another change to the way 'show' displays objects
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another change to the way 'show' displays objects
changed vignette, 'show' method of some objects
added docs for dataset
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Changed biocViews entry of Statistics to Bioinformatics.
initial changes to vignette
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add R files
fixed problem in examples, added 4 text files (eventually for vignette)
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Common dispersion on phi and delta scales added to output for alpha.approxeb
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Updated DGEList function in classes.R to order data by group
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Updated DGEList function in classes.R to order data by group
Resolving changes from unique() ---> levels(); topTags.R changed so more robust
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fixed a few examples that were affected by the unique() ---> levels() change
Changed unique() to levels() in a bunch of cases
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Files and documentation for two new functions, splitIntoGroups and splitIntoGroupsPseudo added
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Major changes: package extended to multiple groups
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added Davis as maintainer
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fixed rounding issue (thanks tom hardcastle)
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fixed rounding issue (thanks tom hardcastle)
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Fixed the version numbers for edgeR (devel and release).
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Fixed the version numbers for edgeR (devel and release).
fixed bug in show method of deDGEList -- change version
fixed bug in show method of deDGEList
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Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
fixed global variable warning
fixed bug when maximizing weighted likelihood
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Bumping the version number for release prep.
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version 0.1.8
changed floor to round -- fixes the pval=0 problem in ridiculous circumstances
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updated LGPL version
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updated LGPL version
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made automatic y-axis scale for MA plots
made automatic y-axis scale for MA plots
more modifications to vignette
add plotMA.R
add plotMA.Rd
fixed code/doc inconsistency
fixed dumb error in Sweave vignette file
fixed verbose output, fixed topTags error when n large
added plotMA, added doPoisson argument to deDGE, changes examples in vignette
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cast the data into matrix class (to avoid some weirdness on data frames)
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added a few checks on DGEList objects
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added a few checks on DGEList objects
changed version number
changed documentation to call constructor
added getData accessor documentation
added getData accessor
changed the vignette to call DGEList constructor
added constructor for DGEList
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This adds 6 new packages to the repository and manifest.
The new packages are: MEDME, edgeR, PLPE, logitT, ArrayTools and
microRNA.
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