1. Biobase
  2. NEWS
Browse code

fix & patch .DollarNames for RStudio

- pattern = "", else fails when called with no first letter
- create and export derived methods, else RStudio does not recognize
inheritance (seems like a bug in RStudio)


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase@129302 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 30/04/2017 14:40:40
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+CHANGES IN VERSION 2.37
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+-----------------------
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+BUG FIXES
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+    o '$' completion on eSet and ExpressionSet works in RStudio.
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 CHANGES IN VERSION 2.33
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 -----------------------
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Browse code

bugfix: exprs<- validates dim, dimnames

- https://support.bioconductor.org/p/86260/
- some unit tests also created invalid objects


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase@120255 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 18/08/2016 19:23:14
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+-----------------------
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+BUG FIXES
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+    o exprs<- enforces value with correct dim, dimnames.
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 CHANGES IN VERSION 2.31
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 -----------------------
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Browse code

feature: tail.AnnotatedDataFrame, too

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase@111612 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 18/12/2015 02:08:58
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 NEW FEATURES
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     o tab completion implemented for eSet classes
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-    o head.AnnotatedDataFrame method introduced
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+    o head and tail.AnnotatedDataFrame methods introduced
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 CHANGES IN VERSION 2.27
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 -----------------------
Browse code

feature: head.AnnotatedDataFrame

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase@111607 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 18/12/2015 00:44:47
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 NEW FEATURES
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     o tab completion implemented for eSet classes
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+    o head.AnnotatedDataFrame method introduced
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 CHANGES IN VERSION 2.27
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 -----------------------
Browse code

implement .DollarNames.eSet

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase@111207 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 04/12/2015 14:18:22
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+-----------------------
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+
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+NEW FEATURES
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+    o tab completion implemented for eSet classes
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Browse code

Add write.AnnotatedDataFrame

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase@99909 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 27/02/2015 02:23:52
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-BUG FIXES
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+NEW FEATURES
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-    o Updating an AnnotatedDataFrame no longer duplicates metadata
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-      from partially matching column names.
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+    o Add write.AnnotatedDataFrame function; request of
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+    samuel.granjeaud
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 CHANGES IN VERSION 2.21
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     o NChannelSet validity requires all assayDataElementNames() to be
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       levels in varMetadata()$channel.
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+BUG FIXES
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+
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+    o Updating an AnnotatedDataFrame no longer duplicates metadata
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+      from partially matching column names.
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 CHANGES IN VERSION 2.19
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 -----------------------
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Browse code

no partial name match when updating AnnotatedDataFrame metadata

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase@86611 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 20/02/2014 01:44:19
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 CHANGES IN VERSION 2.21
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 -----------------------
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+BUG FIXES
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+    o Updating an AnnotatedDataFrame no longer duplicates metadata
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+      from partially matching column names.
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+
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+CHANGES IN VERSION 2.21
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+-----------------------
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+
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 USER VISIBLE CHANGES
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     o channelNames<-,NChannelSet,*-methods allow re-naming channels
Browse code

stronger channelNames / assayDataElementNames validity

- flexible when retrieving channelNames for backward compatiblity


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase@77311 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 10/06/2013 15:37:33
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     o channelNames<-,NChannelSet,*-methods allow re-naming channels
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+    o NChannelSet validity requires all assayDataElementNames() to be
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+      levels in varMetadata()$channel.
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+
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 CHANGES IN VERSION 2.19
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 -----------------------
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Browse code

assayData<-,NChannelSet method

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase@76553 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 14/05/2013 20:18:43
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+CHANGES IN VERSION 2.21
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+-----------------------
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+
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+USER VISIBLE CHANGES
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+    o channelNames<-,NChannelSet,*-methods allow re-naming channels
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+
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 CHANGES IN VERSION 2.19
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 -----------------------
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Browse code

dimnames, dimnames<- and corresponding rownames, colnames on eSet

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase@71499 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 27/11/2012 22:28:12
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+CHANGES IN VERSION 2.19
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+-----------------------
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+
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+USER VISIBLE CHANGES
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+    o dimnames(), rownames(), colnames() and setters work on
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+    eSet-derived objects
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 CHANGES IN VERSION 2.17
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 -----------------------
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Browse code

allow dimnames(elt) to be NULL in assayDataNew

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase@66592 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 11/06/2012 21:03:15
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-CHANGES IN VERSION 2.17.5
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+CHANGES IN VERSION 2.17
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 -----------------------
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     o l2e(), previously deprecated, has been made defunct.
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-CHANGES IN VERSION 2.17.1
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-
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-
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     o All objects made defunct in previous release cycles have been removed.
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       This includes geneNames, getExpData, eList, reporterNames, getBiocRepos,
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       read.exprSet, updateOldMiame, df2pD, read.pD, read.phenoData, exprData,
Browse code

Previously deprecated function l2e() has been made defunct.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase@65430 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 26/04/2012 00:09:28
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+-----------------------
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+
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+
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+    o l2e(), previously deprecated, has been made defunct.
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+
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 CHANGES IN VERSION 2.17.1
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 ----------------------
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Browse code

Once again removing functions and classes marked defunct, but this time not still exporting the phenoData and phenoData<- methods which are not defunct (though the phenoData class is).

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase@65246 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 18/04/2012 19:05:17
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+----------------------
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+
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+USER VISIBLE CHANGES
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+
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+    o All objects made defunct in previous release cycles have been removed.
7 
+      This includes geneNames, getExpData, eList, reporterNames, getBiocRepos,
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+      read.exprSet, updateOldMiame, df2pD, read.pD, read.phenoData, exprData,
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+      exprList, and phenoData.
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+
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 CHANGES IN VERSION 2.11
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 ----------------------
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Browse code

rolling back to r65233 because many packages depend on the defunct functions removed there

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase@65239 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 18/04/2012 16:57:35
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-      This includes geneNames, getExpData, eList, reporterNames, getBiocRepos,
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-      read.exprSet, updateOldMiame, df2pD, read.pD, read.phenoData, exprData,
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-      exprList, and phenoData.
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-
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 ----------------------
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Browse code

Cleanup: remove classes and functions deprecated in a previous release cycle, cleanup partial argument NOTEs, resave data files for maximum compression

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase@65234 bc3139a8-67e5-0310-9ffc-ced21a209358

Dan Tenenbaum authored on 17/04/2012 23:32:43
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+
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+
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+    o All objects made defunct in previous release cycles have been removed.
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+      This includes geneNames, getExpData, eList, reporterNames, getBiocRepos,
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+      read.exprSet, updateOldMiame, df2pD, read.pD, read.phenoData, exprData,
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+      exprList, and phenoData.
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+
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 CHANGES IN VERSION 2.11
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 ----------------------
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Browse code

better error message when varMetadata<-,AnnotatedDataFrame tries to update invalid column(s)

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase@51575 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 16/12/2010 18:59:58
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     o  MIAME class moved to subclass of MIAxE virtual class
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-
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     o Added MIAxE virtual class to hold experiment meta-data classes
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Browse code

- Added MIAxE virtual class to hold metadata for experiments - MIAME class is now a subclass of MIAxE - Bumped versions for eSet, ExpressionSet and MIAME objects

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase@50582 bc3139a8-67e5-0310-9ffc-ced21a209358

Valerie Obenchain authored on 01/11/2010 03:55:24
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-    o 'l2e' deprecated, use 'list2env' in base instead.
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Browse code

Deprecated 'l2e' function. Use 'list2env' in base instead.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase@50566 bc3139a8-67e5-0310-9ffc-ced21a209358

Valerie Obenchain authored on 29/10/2010 22:19:58
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     o 'snpCall' 'snpCallProbability' accessors added for SnpSet.
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 BUG FIXES
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     o 'selectSome' returns short factors as character()
Browse code

update selectSome() to return character() on short factor (as advertised) update NEWS to print correctly with news(package='Biobase')

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase@44936 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 28/02/2010 22:39:00
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-        **************************************************
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-        *                                                *
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-        *              2.11 SERIES NEWS                   *
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-        *                                                *
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-        **************************************************
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+----------------------
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-        **************************************************
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-        *                                                *
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-        *              2.10 SERIES NEWS                   *
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-        *                                                *
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     o 'sampleNames,NChannelSet-method' returns a vector when the
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     sample names of each channel are the same.
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-        **************************************************
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-        *                                                *
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-        *              2.8 SERIES NEWS                   *
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-        *                                                *
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+----------------------
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 NEW FEATURES
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     o openPDF now checks for NULL or zero-length pdfviewer option
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-        **************************************************
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-        *                                                *
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-        *              2.7 SERIES NEWS                   *
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-        *                                                *
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-        **************************************************
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+----------------------
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 NEWLY DEFUNCT CLASSES, METHODS, FUNCTIONS, DATA SETS
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     o Defunct S4 Classes
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-       1) annotatedDataset - class definition still exits to support phenoData conversion
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+       1) annotatedDataset - class definition still exits to support
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+       phenoData conversion
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        2) exprMatrix - removed class definition
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-       3) exprSet - class definition still exists to allow conversion to ExpressionSet
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-       4) phenoData - class definition still exists to allow conversion to AnnotatedDataFrame
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+       3) exprSet - class definition still exists to allow conversion
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+       to ExpressionSet
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+       4) phenoData - class definition still exists to allow
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+       conversion to AnnotatedDataFrame
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     o Defunct Generics/Methods
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        1) addVarMetadataEntry - S4 generic definition removed
Browse code

update vignette to mention protocolData, AnnotationDbi (thanks Elmar) update show,eSet-method - display protocolData - don't display AnnotatedDataFrame detail if empty update cache man page to correctly escape '.' in example

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase@43708 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 22/12/2009 19:46:28
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+    o 'show,eSet-method' summarizes protocolData, if available.
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         **************************************************
Browse code

add snpCall, snpCall<-, snpCallProbability, snpCallProbability<- for SnpSet

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase@43407 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 05/12/2009 13:15:26
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+        **************************************************
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+        *                                                *
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+        *                                                *
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         **************************************************
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         *              2.10 SERIES NEWS                   *
Browse code

Removed scanDate slot from eSet and replaced it with protocolData slot. Also updated eSet objects and bumped package version numbers.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase@40809 bc3139a8-67e5-0310-9ffc-ced21a209358

Patrick Aboyoun authored on 24/07/2009 03:16:33
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-    o 'scanDates' slot added to eSet class to store a character
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-    set by scanDates<-.
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+    o 'protocolData' slot added to eSet class to store protocol
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+    metadata stored in microarray data files; can be accessed by
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+    protocolData and set by protocolData<-.
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     o 'sampleNames,NChannelSet-method' returns a vector when the
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     sample names of each channel are the same.
Browse code

Updating the NEWS file on the new scanDates slot in eSet.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase@40200 bc3139a8-67e5-0310-9ffc-ced21a209358

Patrick Aboyoun authored on 18/06/2009 01:38:20
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+    set by scanDates<-.
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     o 'sampleNames,NChannelSet-method' returns a vector when the
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     sample names of each channel are the same.
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Browse code

report sampleNames,NChannelSet as vector when sample names are identical across channels

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase@39133 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 25/04/2009 15:30:00
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+        **************************************************
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+        *                                                *
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+        *              2.10 SERIES NEWS                   *
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+        *                                                *
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+        **************************************************
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+    o 'sampleNames,NChannelSet-method' returns a vector when the
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+    sample names of each channel are the same.
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         **************************************************
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         *                                                *
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         *              2.8 SERIES NEWS                   *
Browse code

openPDF checks for pdfviewer NULL or ''

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase@32101 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 03/06/2008 16:41:56
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+
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         **************************************************
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         *                                                *
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         *              2.7 SERIES NEWS                   *
Browse code

NEWS for makeDataPacakge

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase@31846 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 21/05/2008 13:19:45
Showing 1 changed files
NEWS
History View file @ c6c1ed4
... ... 
@@ -4,6 +4,11 @@
4 4 
         *                                                *
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         **************************************************
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+NEW FEATURES
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+
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+    o 'makeDataPacakge' method for ExpressionSet now accepts a
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+    'description' argument for the generated manual page.
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+
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 BUG FIXES
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     o combine,matrix,matrix-method would record 'NA' for entries in
Browse code

combine,matrix,matrix-method bug fix - non-overlapping rows and columns in the second matrix were NA, rather than the value in the second matrix - typo in vignett

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase@31471 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 02/05/2008 00:20:41
Showing 1 changed files
NEWS
History View file @ 9510ad4
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@@ -1,3 +1,15 @@
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+        **************************************************
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+        *                                                *
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+        *              2.8 SERIES NEWS                   *
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+        *                                                *
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+        **************************************************
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+
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+BUG FIXES
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+
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+    o combine,matrix,matrix-method would record 'NA' for entries in
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+    the second matrix with niether rows nor columns present in the
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+    first.
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+
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         **************************************************
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         *                                                *
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         *              2.7 SERIES NEWS                   *
Browse code

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'


git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase@31215 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 20/04/2008 16:35:41
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NEWS
History View file @ 2a6d5b2
... ... 
@@ -9,6 +9,9 @@ SIGNIFICANT USER-VISIBLE CHANGES
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     o 'combine' on data.frame columns with mismatched levels causes a
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     warning, rather than error.
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+    o updateObject does not warn about duplicating locked environment,
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+    unlesss verbose=TRUE
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+
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 NEW FEATURES
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     o 'combine' now works to combine rows of ExpressionSet
Browse code

eSet AnnotatedDataFrame created with 'featureColumns' spelt incorrectly NEWS from previous change to combine

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase@30926 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 08/04/2008 19:39:13
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NEWS
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@@ -11,7 +11,7 @@ SIGNIFICANT USER-VISIBLE CHANGES
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 NEW FEATURES
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-    o None
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+    o 'combine' now works to combine rows of ExpressionSet
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 BUG FIXES
17 17
Browse code

Large undertaking to make classes exprSet and phenoData classes defunct. See NEWS file for more information.

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase@30343 bc3139a8-67e5-0310-9ffc-ced21a209358

Patrick Aboyoun authored on 04/03/2008 00:35:06
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NEWS
History View file @ 6580313
... ... 
@@ -9,7 +9,6 @@ SIGNIFICANT USER-VISIBLE CHANGES
9 9 
     o 'combine' on data.frame columns with mismatched levels causes a
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     warning, rather than error.
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-
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 NEW FEATURES
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     o None
... ... 
@@ -17,4 +16,49 @@ NEW FEATURES
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 BUG FIXES
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     o AnnotatedDataFrame 'show' listed additional varMetadata column
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-      names incorrectly when labelDescription was not thie first.
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+      names incorrectly when labelDescription was not the first.
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+
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+NEWLY DEFUNCT CLASSES, METHODS, FUNCTIONS, DATA SETS
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+
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+    o Defunct S4 Classes
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+       1) annotatedDataset - class definition still exits to support phenoData conversion
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+       2) exprMatrix - removed class definition
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+       3) exprSet - class definition still exists to allow conversion to ExpressionSet
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+       4) phenoData - class definition still exists to allow conversion to AnnotatedDataFrame
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+
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+    o Defunct Generics/Methods
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+       1) addVarMetadataEntry - S4 generic definition removed
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+       2) as.data.frame.exprSet - S3 method removed
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+       3) convertVarLabels - S4 generic definition removed
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+       4) eList - S4 methods remain with .Defunct messages
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+       5) "eList<-" - S4 methods remain with .Defunct messages
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+       6) exprs2excel - S4 generic definition removed
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+       7) getExpData - S4 methods remain with .Defunct messages
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+       8) geneNames - S4 methods remain with .Defunct messages
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+       9) "geneNames<-" - S4 methods remain with .Defunct messages
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+      10) getUnits - S4 generic definition removed
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+      11) getVarMetadata - S4 generic definition removed
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+      12) iter - S4 generic definition removed
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+      13) reporterInfo - S4 generic definition removed
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+      14) "reporterInfo<-" - S4 generic definition removed
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+      15) reporterNames - S4 methods remain with .Defunct messages
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+      16) "reporterNames<-" - S4 methods remain with .Defunct messages
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+      17) split (for use with exprSet objects) - S4 generic definition removed
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+      18) update2MIAME - S4 generic definition removed
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+
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+    o Defunct functions
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+       1) df2pD - function stub with .Defunct message
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+       2) read.exprSet - function stub with .Defunct message
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+       3) read.pD - function stub with .Defunct message
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+       4) read.phenoData - function stub with .Defunct message
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+       5) updateOldMiame - function stub with .Defunct message
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+
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+    o Defunct data sets
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+       1) bbsym
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+       2) eset - use sample.ExpressionSet instead
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+       3) golubMergeSub
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+       4) sample.eSet - use sample.MultiSet instead
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+       4) sample.exprSet.1 - use sample.ExpressionSet instead
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+       5) sample.exprSet - use sample.ExpressionSet instead
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+       6) SWPD
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+       7) swrep
Browse code

Show correct varMetadata column names when labelDescription is in a column other than the first

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase@30269 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 28/02/2008 22:36:57
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NEWS
History View file @ 06ef4e1
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@@ -16,4 +16,5 @@ NEW FEATURES
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 BUG FIXES
18 18
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-
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+    o AnnotatedDataFrame 'show' listed additional varMetadata column
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+      names incorrectly when labelDescription was not thie first.
Browse code

- data.frame(x=I()) replaced with data.frame(x=,stringsAsFactors=FALSE) - added 'Bug fixes' section to NEWS

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase@29962 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 12/02/2008 13:43:55
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NEWS
History View file @ eec8ce7
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@@ -13,3 +13,7 @@ SIGNIFICANT USER-VISIBLE CHANGES
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 NEW FEATURES
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     o None
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+
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+BUG FIXES
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+
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+
Browse code

- Add a 'NEWS' file - error message tweak for initialize,eSet-method - BiobaseDevelopment.Rnw typo

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/Biobase@29914 bc3139a8-67e5-0310-9ffc-ced21a209358

Martin Morgan authored on 09/02/2008 14:39:24
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NEWS
History View file @ 7c6b704
1 1 
new file mode 100644
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@@ -0,0 +1,15 @@
1 
+        **************************************************
2 
+        *                                                *
3 
+        *              2.7 SERIES NEWS                   *
4 
+        *                                                *
5 
+        **************************************************
6 
+
7 
+SIGNIFICANT USER-VISIBLE CHANGES
8 
+
9 
+    o 'combine' on data.frame columns with mismatched levels causes a
10 
+    warning, rather than error.
11 
+
12 
+
13 
+NEW FEATURES
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+
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+    o None