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Bioconductor Changlog.
Wed, 03 Jun 2009
explorase
Do not take initial entity type from a list file name (which has no
entity type). Also, ensure entity type exists before setting it as
current type.
explorase
Tweak to exp_loadFiles() contract, add docs.
Version bump.
Better heuristic for guessing experimental factors.
Fix several bugs in file loading. Error dialog shown when file type
cannot be automatically determined.
explorase
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
explorase
Removing support for explorase on pitt (ggobi issue).
explorase
Comment out exp_loadNetwork.
explorase
Add MA plot functionality, courtesy of Teng Fei, and some extremely
experimental network support.
explorase
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
explorase
Added support for Mac OS X.
Add missing documentation, pass R CMD check. Change
lawremi@iastate.edu -> mflawren@fhcrc.org. Bump version.
explorase
Documentation tweaks and version bump.
Small bug fixes.
explorase
Bump version to 1.5.2.
Make entity selection via lists a bit more intuitive (selection from
list overrides current selection in table, multiple lists may be
selected). Allow importing of empty lists.
Add support for directly importing an ExpressionSet.
Also add notes on future plans.
explorase
Do not treat '#' as comment character when loading data. Set current
entity type from type of first file when loading a project (or
importing a file).
explorase
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
Bump version to 1.3.8.
Fix limma interface for designs with factors with levels not represented
by a factor value.
explorase
Clean .csv file extension when naming the GGobi dataset.
explorase
- Update filter column combobox when list name changes.
- Make S expressions in filter dialog work.
Remove BioC support for Mac OS X build of explorase.
explorase
Revert change to use X11 cairo support, as that is X11-specific, while
cairoDevice works on Windows.
explorase
Remove require(limma) call (we now import limma), remove exp_loadNetwork
(for now) and make exp_brushColor non-public (now called
getBrushColor).
explorase
Removed dependence on gtkDevice in favor of X11(type = "cairo") from grDevices package.
explorase
Make Refresh button insensitive after refresh.
Make capitalization consistent in Limma front-end.
Make backwards compatible with non-csv suffixed files.
Clicking on a node in the ggtree now brushes the descendent leaves.
Use .csv as final extension for lists, info, data and design. Disable
'Find' button in 'Find Patterns' until 'Refresh' is pressed after the
cutoff has been adjusted. Add 'cor-p-values' output option for
outputting the corrected p-values. FDR is now the default p-value
correction method.
explorase
Permit replicate averaging after analysis. Remember experimental
data type when matrix passed via explorase() function. Remove stray
browser().
explorase
Fix NAMESPACE importing now nonexistent package biocola.
explorase
Import dependencies (rather than depend on them). Be more robust to
white space and other errors in input files. Move toward network
support. Output coefficients and fitted values from limma. Default to no
p-value adjustment for limma. Handle custom entity types better.