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Bioconductor Changlog.
Thu, 18 Jun 2009
ACME
Added scanDate slot to Biobase's eSet class, added functionality in affy to utilize the new scanDate slot and updated all the packages that create direct subclasses of eSet, ExpressionSet or NChannelSet.
ACME
Bumped version in DESCRIPTION to catch last changes
Added Biobase and methods to depends to deal with CHECK errors.
Used assign rather than <<- in findClosestGene.R to clean up
lack of refflat in .GlobalEnv the first time used.
ACME
changed imports to exclude biobase and methods in DESCRIPTION file
ACME
Added stats(start,end) and graphics(plot) to imports. Removed a
few redundant imports from Biobase. Vignette now builds fine.
changed a variable name in vignette to match previously assigned variable
ACME
Added documentation for generics and methods.
Added documentation for new classes, ACMESet and ACMECalcSet.
Removed stray browser() in ACMECalcSet validity method.
Import Biobase explicitly and fully to deal with the necessity
to have all methods defined on ExpressionSet and friends.
2.1.0
=====
Large number of changes.
* Added ACMESet and ACMECalcSet, based on ExpressionSet
* Converted all code to use new classes
* Fixed bug in findClosestGene that caused function to fail
if refflat already existed in the global namespace
* Fixed "one-sample" bug (actually a side-effect of new classes)
* Fixed handling of NAs so that do.aGFF.calc will deal with them
* Changed vignette to use new classes
ACME
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
ACME
Changed biocViews entry of Statistics to Bioinformatics.
ACME
added URL
ACME
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
ACME
open gzfile to work on windows; close opened connection when done.
ACME
Removed usage (or reference) to pstricks tex style in BioC vignettes.
ACME
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
ACME
Removed psfig from \usepackage{} in the .Rnw file of the following packages: MeasurementError.cor, GEOquery, rama, marray, aCGH, multtest, nnNorm, RMAGEML, ACME and bridge. Psfig/TeX was actually not needed by these vignettes. Besides Psfig/TeX has licensing issues and will be removed from our build machines.