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Bioconductor Changlog.
Tue, 13 Oct 2009
pdInfoBuilder
Prep'ing to add 2nd version of db-based annotation
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pdInfoBuilder
Fixed merging of POS and NDF files
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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.
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pdInfoBuilder
Improving support to Gene/Exon Arrays - gene level summaries
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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
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pdInfoBuilder
Implemented changes to accommodate sequence methods that depend on biostrings/iranges. Improved templates so the final object passes check
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pdInfoBuilder
Added support to HT_HGU_133+ Array
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pdInfoBuilder
Updated imports for Affymetrix Annotations v24, aka NA24
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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
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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
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pdInfoBuilder
Fixed sorting schema for sequences
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pdInfoBuilder
chipName and ALLELE fix
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pdInfoBuilder
Added vignette explaining how to build packages for several array types
Added diagn. messages. Fixed chipName method for NGS arrays
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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)
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pdInfoBuilder
Updated chrom info in featureSet for NGS and fixed pmChr accessor
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pdInfoBuilder
Much better support to Exon/Gene Arrays
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pdInfoBuilder
Updated vignette
Added warnings, so users don't expect SNP packages without CRLMM data to work with CRLMM
[/pdInfoBuilder] permanent link
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
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pdInfoBuilder
Removing un-needed classes
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pdInfoBuilder
Bug fixes so that this will hopefully pass check.
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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.
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pdInfoBuilder
Fixed bug in UnitTests for SNP 5/6
Fixed bugs in UnitTests
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pdInfoBuilder
Adding support to Affymetrix GeneST Arrays
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pdInfoBuilder
Multiple fixes: tiling ngs with XYS, missing fields on tables
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pdInfoBuilder
Cleaning up pkg
Improved support for NimbleGen Expression Arrays
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pdInfoBuilder
Replaced XDataFrame with DataFrame to reflect changes in IRanges.
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pdInfoBuilder
Attempt to add an extra SNP/CNV level class
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pdInfoBuilder
doc change indicating parms_store instead of data_store for certain components
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pdInfoBuilder
pass check -- ST seed needs more doc
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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
pdInfoBuilder
Prep'ing to add 2nd version of db-based annotation
[/pdInfoBuilder] permanent link
pdInfoBuilder
added new template package
added new function getGeometry
start of some changes to affy ST, tiling and expression arrasy
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pdInfoBuilder
work on affy tiling and ST arrays, updated man pages
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pdInfoBuilder
Updating support for NGS Tiling Arrays - contributed by Matt Settles msettles@wsu.edu
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pdInfoBuilder
Fixed merging of POS and NDF files
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pdInfoBuilder
Bumping version numbers for BioC 2.4 devel.
Bumping version numbers for BioC 2.3 release.
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pdInfoBuilder
Added NimbleGen Tiling Example to the vignette
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pdInfoBuilder
Cleaning up
Fixing requirements for RMA on Exon arrays
Improved support for Affy Exon arrays
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pdInfoBuilder
Adding structure for version 2 of pdInfoBuilder
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pdInfoBuilder
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
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