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Bioconductor Changlog.
Sat, 06 Jun 2009
edgeR
1 June 2009, edgeR 1.3.3
- paste() replaced with file.path() in vignette.
edgeR
add a few more checks to the DGEList constructor
edgeR
small modifications to 'exactTestNB' defaults
edgeR
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
edgeR
another change to the way 'show' displays objects
edgeR
another change to the way 'show' displays objects
changed vignette, 'show' method of some objects
added docs for dataset
edgeR
Changed biocViews entry of Statistics to Bioinformatics.
initial changes to vignette
edgeR
add R files
fixed problem in examples, added 4 text files (eventually for vignette)
edgeR
Common dispersion on phi and delta scales added to output for alpha.approxeb
edgeR
Updated DGEList function in classes.R to order data by group
edgeR
Updated DGEList function in classes.R to order data by group
Resolving changes from unique() ---> levels(); topTags.R changed so more robust
edgeR
fixed a few examples that were affected by the unique() ---> levels() change
Changed unique() to levels() in a bunch of cases
edgeR
Files and documentation for two new functions, splitIntoGroups and splitIntoGroupsPseudo added
edgeR
Major changes: package extended to multiple groups
edgeR
added Davis as maintainer
edgeR
fixed rounding issue (thanks tom hardcastle)
edgeR
fixed rounding issue (thanks tom hardcastle)
edgeR
Fixed the version numbers for edgeR (devel and release).
edgeR
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
edgeR
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
edgeR
Bumping the version number for release prep.
edgeR
version 0.1.8
changed floor to round -- fixes the pval=0 problem in ridiculous circumstances
edgeR
updated LGPL version
edgeR
updated LGPL version
edgeR
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
edgeR
cast the data into matrix class (to avoid some weirdness on data frames)
edgeR
added a few checks on DGEList objects
edgeR
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
edgeR
This adds 6 new packages to the repository and manifest.
The new packages are: MEDME, edgeR, PLPE, logitT, ArrayTools and
microRNA.