About
Click here
to learn more about this blog.
Packages
Click on a link
for updates to that package only.
Subscribe
Subscribe to the
Bioconductor Changlog.
Tue, 13 Oct 2009
oligoClasses
added a methods dependency - se if that gets the warnings down
[/oligoClasses] permanent link
oligoClasses
Cleaning up code
[/oligoClasses] permanent link
oligoClasses
changed some of the validity checks for oligoSnpSet
[/oligoClasses] permanent link
oligoClasses
Fixing a man page link to Biobase.
Added the Biobase package to link specification for Biobase classes.
[/oligoClasses] permanent link
oligoClasses
Adding support to Affymetrix GeneST Arrays
[/oligoClasses] permanent link
oligoClasses
Bug fix: initialize for SnpCopyNumberSet
[/oligoClasses] permanent link
oligoClasses
updated setValidity methods for snp-level set objects
[/oligoClasses] permanent link
oligoClasses
fixed db method for SnpLevelSet
added a check for the annotation package in the db method. Export db, chromosome and position
added man pages for chromosome and position
added accessors for feature information for SnpLevelSet
[/oligoClasses] permanent link
oligoClasses
Cleaning up docs
Cleaning up docs
Fixed warnings from CHECK
Generalized bg/bgindex methods for FeatureSet objects
[/oligoClasses] permanent link
oligoClasses
fixed bug in calculateCopyNumber
[/oligoClasses] permanent link
oligoClasses
minor updates, correct man build warnings
[/oligoClasses] permanent link
oligoClasses
Fixed problems with sampleNames, which caused rma() to fail
[/oligoClasses] permanent link
oligoClasses
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
[/oligoClasses] permanent link
oligoClasses
Cleaning up
[/oligoClasses] permanent link
oligoClasses
hopefully fixed missing links error for eSet and versioned classes in the Rd files for SnpLevelSet and GeneSTFeatureSet
[/oligoClasses] permanent link
oligoClasses
Cleaning up code
[/oligoClasses] permanent link
oligoClasses
Added TilingFeatureSet2 class to handle 2-colors applications of tiling arrays. Redefined the FeatureSet class and sampleNames method. Removed unused class.
[/oligoClasses] permanent link
oligoClasses
need to load tools for the vignette to work
[/oligoClasses] permanent link
oligoClasses
Sorted indices for bg probes
[/oligoClasses] permanent link
oligoClasses
Fixing accessors for coordinates
[/oligoClasses] permanent link
oligoClasses
several updates to calculateCopyNumber. Added validObject() check to combine method
[/oligoClasses] permanent link
oligoClasses
Improving support for Exon/Gene arrays
[/oligoClasses] permanent link
oligoClasses
added vignette for snp-level classes. updated man page for SnpLevelSet-class.
[/oligoClasses] permanent link
oligoClasses
Bumping versions...
Moving accessors from oligo to oligoClasses - Improving documentation
[/oligoClasses] permanent link
oligoClasses
fixed undocument s4 method warning
[/oligoClasses] permanent link
oligoClasses
Fixed problems with sampleNames, which caused rma() to fail
[/oligoClasses] permanent link
oligoClasses
Removed scanDate slot from eSet and replaced it with protocolData slot. Also updated eSet objects and bumped package version numbers.
[/oligoClasses] permanent link
oligoClasses
Adding structure for version 2 of pdInfoBuilder
[/oligoClasses] permanent link
oligoClasses
Prep'ing to add 2nd version of db-based annotation
[/oligoClasses] permanent link
oligoClasses
Fixed documentation after moving some methods from oligo to oligoClasses
[/oligoClasses] permanent link
oligoClasses
FIxed mmSeqeuence for SNP chips
[/oligoClasses] permanent link
oligoClasses
Improved NAMESPACE / Added basicRMA()
Implemented changes to accommodate sequence methods that depend on biostrings/iranges. Improved templates so the final object passes check
[/oligoClasses] permanent link
oligoClasses
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
[/oligoClasses] permanent link
oligoClasses
Moved many accessors from oligo to oligoClasses. Improving organization, prep'ing to add more meaningful documentation
[/oligoClasses] permanent link
oligoClasses
Removed scanDate slot from eSet and replaced it with protocolData slot. Also updated eSet objects and bumped package version numbers.
[/oligoClasses] permanent link
oligoClasses
Reformatted the Licence information in DESCRIPTION files to bring them into compliance.
[/oligoClasses] permanent link
oligoClasses
Improving support to Gene/Exon Arrays - gene level summaries
[/oligoClasses] permanent link
oligoClasses
Improved support for NimbleGen Expression Arrays
[/oligoClasses] permanent link
oligoClasses
changed the chromosome and position methods for SnpLevelSet -- should work for combined objects
added a method to combine instances of classes that extend SnpLevelSet
[/oligoClasses] permanent link
oligoClasses
added method to coerce SnpCallSetPlus to oligoSnpSet. Added functions calculateCopyNumber and affyPlatforms
[/oligoClasses] permanent link