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Bioconductor Changlog.
Tue, 13 Oct 2009
edgeR
Updated DGEList function in classes.R to order data by group
Resolving changes from unique() ---> levels(); topTags.R changed so more robust
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
Files and documentation for two new functions, splitIntoGroups and splitIntoGroupsPseudo added
edgeR
This update introduces two new functions, equaliseLibSizes and estimateCommonDisp, to edgeR. equaliseLibSizes takes a DGEList object and a fixed value for phi and adjusts the count data so that library sizes are approximately equal. It contains code from quantileAdjust, but no iterative procedures. If the argument phi is set to 0, then the Poisson model is used to equalise the libraries. Allowing for phi to be an argument required some modifications to be made to interpolateHelper. estimateCommonDisp takes fixed count data, assuming library sizes are equal (i.e. pseudodata generated by equaliseLibSizes), and estimates the common dispersion parameter. This function is based on findMaxD2, with the option for using Newton-Raphson feasible for use here, as estimates from NR method that fall outside the (0,1) domain for delta are corrected using a grid search. This fix should probably be applied to findMaxD2. Documentation for interpolateHelper has been extended, but no documentation files have been provided for the two new functions.
edgeR
1 June 2009, edgeR 1.3.3
- paste() replaced with file.path() in vignette.
edgeR
updated LGPL version
edgeR
updated LGPL version
edgeR
Poor man's quantile adjustment functions.
edgeR
another change to the way 'show' displays objects
edgeR
fixed a few examples that were affected by the unique() ---> levels() change
Changed unique() to levels() in a bunch of cases
edgeR
Deleted equaliseLibSizes and estimateCommonDisp as they are not documented
Deleted files without documentation - equaliseLibSizes, estimateCommonDisp, q2qnbinom, qnbinom qpoispm
edgeR
fixed rounding issue (thanks tom hardcastle)
edgeR
Changed biocViews entry of Statistics to Bioinformatics.
initial changes to vignette
edgeR
cast the data into matrix class (to avoid some weirdness on data frames)
edgeR
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
edgeR
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
edgeR
Moving comment lines around.
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
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
small modifications to 'exactTestNB' defaults
edgeR
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
edgeR
Biobase package in Imports: instead of Depends: field.
edgeR
Deleted equaliseLibSizes and estimateCommonDisp as they are not documented
edgeR
add a few more checks to the DGEList constructor
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
Biobase package in Imports: instead of Depends: field.
edgeR
added a few checks on DGEList objects
edgeR
Fixed the version numbers for edgeR (devel and release).
edgeR
another change to the way 'show' displays objects
changed vignette, 'show' method of some objects
added docs for dataset
edgeR
version 0.1.8
changed floor to round -- fixes the pval=0 problem in ridiculous circumstances
edgeR
Major changes: package extended to multiple groups
edgeR
modification to deDGE when doPoisson=TRUE
edgeR
Bumping the version number for release prep.
edgeR
fixed rounding issue (thanks tom hardcastle)
edgeR
added Davis as maintainer
edgeR
This adds 6 new packages to the repository and manifest.
The new packages are: MEDME, edgeR, PLPE, logitT, ArrayTools and
microRNA.
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
Updated DGEList function in classes.R to order data by group