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Bioconductor Changlog.
Tue, 13 Oct 2009
affycomp
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
affycomp
Replaced usage of soon to be defunct class exprSet with ExpressionSet.
affypdnn
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
affypdnn
changes to accommodate adding a name space to affy
affycomp
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
affypdnn
removed quotes from do.call
affycomp
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
affycomp
Removed usage (or reference) to pstricks tex style in BioC vignettes.
affypdnn
Moved 2 of the packages in Depends to Suggests
affypdnn
Modification to make R CMD check run faster
- Added dataset with precomputed values
- Added man page for that dataset
- Bumped version number
affypdnn
typos in the vignette
affypdnn
Propagated fixes to the changes made in the release 2.2 branch
(revision 31982)
affycomp
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
affycomp
Removed pch from matplot in affycomp.figure6a
affycomp
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
affypdnn
added citation
Added the mandatory vignette.
bumping up version number
Fix in "pdnn.scalevalue.exprSet"
affypdnn
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
affycomp
fixed parser errors and incremented version number
affypdnn
Replaced usage of defunct class exprSet with ExpressionSet.
affypdnn
- fixed typo in man page
- bumped version number
affycomp
Replaced data() by getData() to remove NOTES on 'no visible bindings'; Converted phenoData objects to AnnotatedDataFrame; Replaced geneNames by featureNames
affycomp
Fixed usage of se.exprs in ExpressionSet class.
affypdnn
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
affylmGUI
changes on dashes to ordinary ones
affylmGUI
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
affylmGUI
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
affylmGUI
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
affylmGUI
Changed biocViews entry of Statistics to Bioinformatics.
affylmGUI
Replaced support for defunct class exprSet with ExpressionSet.
affylmGUI
Remove some corrections by P. Aboyoun in main.R. The references to exprSet are needed
to check old data files for class name of exprSet and if present retrieve data from them
without needing the exprSet class definition.
also reformat the layout of some code to my liking.
This version ready for release with Bioconductor 2.2
Change references back to exprSet to allow loading of old data files, without using exprSet objects
Reformatting some code
affylmGUI
Added GUI to DESCRIPTION file.
affylmGUI
Added LazyLoad: yes to DESCRIPTION file
affylmGUI
Ensure line endings in CITATION are LF only - may have been cause of errors(unexpected end of input) on Mac OSX R CMD check
affy
Rolled back r37752. Fixed affydata instead.
Fixed a cel file read issue related to the affydata package.
affy
Small change to bg.correct.mas to allow chips that have some probesets missing MM probes to be processed. Note that this will still result in NA expression values for these probesets.
affy
Removed usage (or reference) to pstricks tex style in BioC vignettes.
affycoretools
Added AnnotationDbi to Imports
[/affycoretools] permanent link
affycoretools
Removed support for soon to be defunct class exprSet.
[/affycoretools] permanent link
affyio
(1.7.8) Minor changes to the pgf/clf parsing code. In particular functionality for assessing whether the required fields in the headers are present.
affy
Fixed creation of .affyInternalEnv to ignore the functions designed to allow updating the AffyBatch methods. Previously we ended up with 'yBatch.methods' as one of the normalize.AffyBatch.methods or 'orrect.methods' as one of the pmcorrect.methods.