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Mon, 21 Apr 2008
GGtools
passing check
oligoClasses
hopefully fixed missing links error for eSet and versioned classes in the Rd files for SnpLevelSet and GeneSTFeatureSet
[/oligoClasses] permanent link
GGBase
minor
minor
minor fixes
ok
starting class doc
LazyLoad yes
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
limma
Forgot to svn 'add' getEAWP.Rd previously.
Biostrings
Minor man file edit.
Added the ability to specify quality measures for the strings when performing pairwise alignments.
explorase
Revert change to use X11 cairo support, as that is X11-specific, while
cairoDevice works on Windows.
oneChannelGUI
Adding a filter for exon-level analysis for geneChipEXON 1.0 ST arrays. ThebiomartFilter uses biomaRt to subset only those gene-level probe sets associated to an entrez Gene ID linked to more than one ensembl transcripts. This filter will limit alternative splicing detection only on annotated alternative spliced transcripts.
[/oneChannelGUI] permanent link
SNPchip
updated man pages to fix missing links on the windows platform check -- HmmPredict and RatioSnpSet classes
XDE
updated vignette pdfs
Biobase
updateObject and BiobaseDevelopment vignette adjustments
updateObject
- now quiet about duplcating lockedEnvironment, unless
verbose=TRUE
Vignette:
- 'Recent' references removed
- ... and verbose passed through in updateObject method example
- variant of 'initialize,SwirlSet-method' allowing it to behave as a
copy constructor; a little sly here, as this is used in later parts
of the vignette and serves to quieten warnings about addition
arguments to 'new' during 'updateObject'
I added a check in AssayDataNew to make it throw an error if it is passed unnamed arguments (before, this would have resulted, in effect, in silently dropping them)
I also removed some frivolous dependencies in ExpressionSetIntroduction.Rnw, esApply.Rnw and Qviews.Rnw on the Latex package "pstricks".