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Bioconductor Changlog.
Wed, 27 May 2009
pdInfoBuilder
Replaced XDataFrame with DataFrame to reflect changes in IRanges.
[/pdInfoBuilder] permanent link
Fri, 01 May 2009
pdInfoBuilder
Fixed merging of POS and NDF files
[/pdInfoBuilder] permanent link
Thu, 30 Apr 2009
pdInfoBuilder
Fixed merging of POS and NDF files
[/pdInfoBuilder] permanent link
Sat, 25 Apr 2009
pdInfoBuilder
Fixed sorting schema for sequences
[/pdInfoBuilder] permanent link
Tue, 21 Apr 2009
pdInfoBuilder
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
[/pdInfoBuilder] permanent link
Fri, 17 Apr 2009
pdInfoBuilder
Cleaning up code
[/pdInfoBuilder] permanent link
Thu, 09 Apr 2009
pdInfoBuilder
Updated vignette
Added warnings, so users don't expect SNP packages without CRLMM data to work with CRLMM
[/pdInfoBuilder] permanent link
Wed, 08 Apr 2009
pdInfoBuilder
Added warnings, so users don't expect SNP packages without CRLMM data to work with CRLMM
Added generic builders for SNP arrays. CRLMM wont work with these folks
[/pdInfoBuilder] permanent link
Tue, 07 Apr 2009
pdInfoBuilder
Fixing documentation and adding generic builder for Affymetrix SNP/CNV arrays
Added some dontrun tags around two man page examples since they show how to interact with non-existant files.
Also, cleaned up the initialize methods a little to hopefully avoid problems when instanciating objects.
[/pdInfoBuilder] permanent link
Thu, 02 Apr 2009
pdInfoBuilder
Attempt to add an extra SNP/CNV level class
[/pdInfoBuilder] permanent link
Mon, 30 Mar 2009
pdInfoBuilder
Removing un-needed classes
[/pdInfoBuilder] permanent link
Sat, 28 Mar 2009
pdInfoBuilder
Added NimbleGen Tiling Example to the vignette
[/pdInfoBuilder] permanent link
Fri, 27 Mar 2009
pdInfoBuilder
Implemented changes to accommodate sequence methods that depend on biostrings/iranges. Improved templates so the final object passes check
[/pdInfoBuilder] permanent link
Thu, 26 Mar 2009
pdInfoBuilder
Implemented changes to accommodate sequence methods that depend on biostrings/iranges. Improved templates so the final object passes check
Fixed props of getGeometry-methods.R
Fixed template so packages created by pdInfoBuilder pass R CMD check
[/pdInfoBuilder] permanent link
Wed, 25 Mar 2009
pdInfoBuilder
Cleaning up package, exporting only used classes
Added TilingFeatureSet2 class to handle 2-colors applications of tiling arrays. Redefined the FeatureSet class and sampleNames method. Removed unused class.
[/pdInfoBuilder] permanent link
Sun, 22 Mar 2009
pdInfoBuilder
Fixed error in vignette compilation
[/pdInfoBuilder] permanent link
Fri, 20 Mar 2009
pdInfoBuilder
Added vignette explaining how to build packages for several array types
Added diagn. messages. Fixed chipName method for NGS arrays
[/pdInfoBuilder] permanent link
Thu, 19 Mar 2009
pdInfoBuilder
Added support to HT_HGU_133+ Array
[/pdInfoBuilder] permanent link
Tue, 17 Mar 2009
pdInfoBuilder
Cleaning up pkg
Improved support for NimbleGen Expression Arrays
[/pdInfoBuilder] permanent link
Wed, 11 Mar 2009
pdInfoBuilder
Much better support to Exon/Gene Arrays
[/pdInfoBuilder] permanent link
Tue, 10 Mar 2009
pdInfoBuilder
Cleaning up
Fixing requirements for RMA on Exon arrays
Improved support for Affy Exon arrays
[/pdInfoBuilder] permanent link
Wed, 25 Feb 2009
pdInfoBuilder
Adding structure for version 2 of pdInfoBuilder
[/pdInfoBuilder] permanent link
Fri, 13 Feb 2009
pdInfoBuilder
Prep'ing to add 2nd version of db-based annotation
[/pdInfoBuilder] permanent link
Thu, 12 Feb 2009
pdInfoBuilder
Prep'ing to add 2nd version of db-based annotation
[/pdInfoBuilder] permanent link
Sat, 07 Feb 2009
pdInfoBuilder
fixed template build error
clean up manuals and makePdinfoPackage, moved common code to functions in utils.R, added new package template (work in progress)
[/pdInfoBuilder] permanent link
Wed, 17 Dec 2008
pdInfoBuilder
Bug fixes so that this will hopefully pass check.
[/pdInfoBuilder] permanent link
Sat, 13 Dec 2008
pdInfoBuilder
Updated chrom info in featureSet for NGS and fixed pmChr accessor
[/pdInfoBuilder] permanent link
Wed, 10 Dec 2008
pdInfoBuilder
work on affy tiling and ST arrays, updated man pages
[/pdInfoBuilder] permanent link
Fri, 05 Dec 2008
pdInfoBuilder
added new template package
added new function getGeometry
start of some changes to affy ST, tiling and expression arrasy
[/pdInfoBuilder] permanent link
Thu, 20 Nov 2008
pdInfoBuilder
Multiple fixes: tiling ngs with XYS, missing fields on tables
[/pdInfoBuilder] permanent link
Wed, 22 Oct 2008
pdInfoBuilder
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
[/pdInfoBuilder] permanent link
Tue, 05 Aug 2008
pdInfoBuilder
Updating support for NGS Tiling Arrays - contributed by Matt Settles msettles@wsu.edu
[/pdInfoBuilder] permanent link
Wed, 14 May 2008
pdInfoBuilder
Fixed problem on description of Affy Tiling Arrays
[/pdInfoBuilder] permanent link
Wed, 30 Apr 2008
pdInfoBuilder
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
[/pdInfoBuilder] permanent link
Sat, 26 Apr 2008
pdInfoBuilder
Ensuring correct class for transcript_cluster_id field Gene ST arrays
Ensuring correct class for crosshyb_type field Gene ST arrays
changing readPgf/readClf to readPgfEnv/readClfEnv
Fixing class nomenclature
[/pdInfoBuilder] permanent link
Fri, 25 Apr 2008
pdInfoBuilder
pass check -- ST seed needs more doc
[/pdInfoBuilder] permanent link
Sat, 22 Mar 2008
pdInfoBuilder
Adding support to Affymetrix GeneST Arrays
[/pdInfoBuilder] permanent link
Wed, 30 Jan 2008
pdInfoBuilder
Fixed bug that caused MM sequences to be inconsistent - particular case: offset 0 SNP [A/T] or [C/G]
Fixed bug which caused MM sequences to be inconsistent - nb: genotype calls via CRLMM are not affected
[/pdInfoBuilder] permanent link
Thu, 24 Jan 2008
pdInfoBuilder
Added extra annotation for CNV probes on SNP 5/6 arrays
[/pdInfoBuilder] permanent link
Tue, 22 Jan 2008
pdInfoBuilder
UnitTests now checks for the existence of RCMD
[/pdInfoBuilder] permanent link