| 1952429d |
CHANGES IN VERSION 2.37
-----------------------
BUG FIXES
o '$' completion on eSet and ExpressionSet works in RStudio.
|
| f03aaefd |
CHANGES IN VERSION 2.33
-----------------------
BUG FIXES
o exprs<- enforces value with correct dim, dimnames.
|
| 956745c3 |
CHANGES IN VERSION 2.31
-----------------------
NEW FEATURES
o tab completion implemented for eSet classes
|
| c9fe9cf8 |
o head and tail.AnnotatedDataFrame methods introduced
|
| 956745c3 |
|
| a60b14aa |
CHANGES IN VERSION 2.27
|
| 0db0d143 |
-----------------------
|
| a60b14aa |
NEW FEATURES
|
| 60f66ff2 |
|
| a60b14aa |
o Add write.AnnotatedDataFrame function; request of
samuel.granjeaud
|
| 60f66ff2 |
CHANGES IN VERSION 2.21
-----------------------
|
| 0db0d143 |
USER VISIBLE CHANGES
o channelNames<-,NChannelSet,*-methods allow re-naming channels
|
| f53861fb |
o NChannelSet validity requires all assayDataElementNames() to be
levels in varMetadata()$channel.
|
| a60b14aa |
BUG FIXES
o Updating an AnnotatedDataFrame no longer duplicates metadata
from partially matching column names.
|
| d5bed422 |
CHANGES IN VERSION 2.19
-----------------------
USER VISIBLE CHANGES
o dimnames(), rownames(), colnames() and setters work on
eSet-derived objects
|
| b4a451ea |
CHANGES IN VERSION 2.17
|
| ce321f9b |
-----------------------
USER VISIBLE CHANGES
o l2e(), previously deprecated, has been made defunct.
|
| 5282df43 |
o All objects made defunct in previous release cycles have been removed.
This includes geneNames, getExpData, eList, reporterNames, getBiocRepos,
read.exprSet, updateOldMiame, df2pD, read.pD, read.phenoData, exprData,
exprList, and phenoData.
|
| 33b8390d |
CHANGES IN VERSION 2.11
----------------------
USER VISIBLE CHANGES
|
| 9b6756d9 |
o 'l2e' deprecated, use 'list2env' in base instead
o MIAME class moved to subclass of MIAxE virtual class
NEW FEATURES
o Added MIAxE virtual class to hold experiment meta-data classes
|
| 33b8390d |
|
| 5d341fec |
CHANGES IN VERSION 2.7
----------------------
|
| 99929164 |
USER VISIBLE CHANGES
|
| ba54f831 |
o 'show,eSet-method' summarizes protocolData, if available.
|
| 99929164 |
o 'snpCall' 'snpCallProbability' accessors added for SnpSet.
|
| 33b8390d |
|
| 5d341fec |
BUG FIXES
o 'selectSome' returns short factors as character()
CHANGES IN VERSION 2.5
----------------------
|
| 36e3dc4a |
USER VISIBLE CHANGES
|
| 7f3040d2 |
o 'protocolData' slot added to eSet class to store protocol
metadata stored in microarray data files; can be accessed by
protocolData and set by protocolData<-.
|
| 41168c59 |
|
| 36e3dc4a |
o 'sampleNames,NChannelSet-method' returns a vector when the
sample names of each channel are the same.
|
| 5d341fec |
CHANGES IN VERSION 2.1
----------------------
|
| 9510ad4e |
|
| c6c1ed49 |
NEW FEATURES
o 'makeDataPacakge' method for ExpressionSet now accepts a
'description' argument for the generated manual page.
|
| 9510ad4e |
BUG FIXES
o combine,matrix,matrix-method would record 'NA' for entries in
the second matrix with niether rows nor columns present in the
first.
|
| e8ce4f40 |
o openPDF now checks for NULL or zero-length pdfviewer option
|
| 5d341fec |
CHANGES IN VERSION 2.0
----------------------
|
| 7c6b7043 |
SIGNIFICANT USER-VISIBLE CHANGES
o 'combine' on data.frame columns with mismatched levels causes a
warning, rather than error.
|
| 2a6d5b29 |
o updateObject does not warn about duplicating locked environment,
unlesss verbose=TRUE
|
| 7c6b7043 |
NEW FEATURES
|
| 8d0b01f7 |
o 'combine' now works to combine rows of ExpressionSet
|
| eec8ce7a |
BUG FIXES
|
| 06ef4e10 |
o AnnotatedDataFrame 'show' listed additional varMetadata column
|
| 65803133 |
names incorrectly when labelDescription was not the first.
NEWLY DEFUNCT CLASSES, METHODS, FUNCTIONS, DATA SETS
o Defunct S4 Classes
|
| 5d341fec |
1) annotatedDataset - class definition still exits to support
phenoData conversion
|
| 65803133 |
2) exprMatrix - removed class definition
|
| 5d341fec |
3) exprSet - class definition still exists to allow conversion
to ExpressionSet
4) phenoData - class definition still exists to allow
conversion to AnnotatedDataFrame
|
| 65803133 |
o Defunct Generics/Methods
1) addVarMetadataEntry - S4 generic definition removed
2) as.data.frame.exprSet - S3 method removed
3) convertVarLabels - S4 generic definition removed
4) eList - S4 methods remain with .Defunct messages
5) "eList<-" - S4 methods remain with .Defunct messages
6) exprs2excel - S4 generic definition removed
7) getExpData - S4 methods remain with .Defunct messages
8) geneNames - S4 methods remain with .Defunct messages
9) "geneNames<-" - S4 methods remain with .Defunct messages
10) getUnits - S4 generic definition removed
11) getVarMetadata - S4 generic definition removed
12) iter - S4 generic definition removed
13) reporterInfo - S4 generic definition removed
14) "reporterInfo<-" - S4 generic definition removed
15) reporterNames - S4 methods remain with .Defunct messages
16) "reporterNames<-" - S4 methods remain with .Defunct messages
17) split (for use with exprSet objects) - S4 generic definition removed
18) update2MIAME - S4 generic definition removed
o Defunct functions
1) df2pD - function stub with .Defunct message
2) read.exprSet - function stub with .Defunct message
3) read.pD - function stub with .Defunct message
4) read.phenoData - function stub with .Defunct message
5) updateOldMiame - function stub with .Defunct message
o Defunct data sets
1) bbsym
2) eset - use sample.ExpressionSet instead
3) golubMergeSub
4) sample.eSet - use sample.MultiSet instead
4) sample.exprSet.1 - use sample.ExpressionSet instead
5) sample.exprSet - use sample.ExpressionSet instead
6) SWPD
7) swrep
|
