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Bioconductor Changlog.
Sat, 07 Jun 2008
Biobase
allow readExpressionSet to have only an 'exprsFile' argument
Biobase
I tried to fix the function addVigs2WinMenu so that it actually adds the
proper vignette title to the GUI menu and not the truncated filename!
Biobase
openPDF checks for pdfviewer NULL or ''
Biobase
NEWS for makeDataPacakge
makeDataPackage gets a 'description' argument
sample.ExpressionSet abstract now claims correctly to be ExpressionSet
Biobase
selectSome explicilty coerces subset on either side of '...' to
character, so factors are now represented correctly
Biobase
AnnotatedDataFrame made more friendly to subclassing
- previously, a subclass would often be coerced to AnnotatedDataFrame
during, e.g., subsetting
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
Biobase
Updating biocReposList for BioC 2.3.
Updating the version number for the trunk post-BioC 2.2 release.
Updating the version number for the BioC 2.2 release.
Biobase
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'
I added a check in AssayDataNew to make it throw an error if it is passed unnamed arguments (before, this would have resulted, in effect, in silently dropping them)
I also removed some frivolous dependencies in ExpressionSetIntroduction.Rnw, esApply.Rnw and Qviews.Rnw on the Latex package "pstricks".
Biobase
added ... to the generic definition for description in order to be able to use it in the flowCore package
Biobase
Removed reference of soon-to-be defunct package arrayMagic from vignette.
Biobase
Try to recover more gracefully (suggesting updateObject) when
mis-spelt dimLabels discovered
eSet AnnotatedDataFrame created with 'featureColumns' spelt incorrectly
NEWS from previous change to combine
Biobase
'combine' can now combine rows, if appropriate
- separate method for combine,matrix,matrix
- combine,AssayData,AssayData now re-dispatches to combine for each element
Biobase
Added an interactive() conditional statement for printing out messages of defunct data sets.
Biobase
checkClass unit test
Biobase
(internal) checkClass now uses 'is', allowing, e.g., S3-style c("baz",
"data.frame") to be recognized as a data.frame
Biobase
(internal) checkClass now uses 'is', allowing, e.g., S3-style c("baz",
"data.frame") to be recognized as a data.frame
Update unit tests to reflect loss of methods for accessing now-defunct
class slots
Biobase
Fixed a typo in the featureData help file.
Provide more informative messages when calling validity methods for classes exprSet and phenoData.
Biobase
Provide more informative messages when calling validity methods for classes exprSet and phenoData.
Large undertaking to make classes exprSet and phenoData classes defunct. See NEWS file for more information.
Biobase
Show correct varMetadata column names when labelDescription is in
a column other than the first
Biobase
Fixed a typo in the deprecation message.
Biobase
futtzing with the print method for notes in an ExpressionSet - really
high yield work :-)
Biobase
- data.frame(x=I()) replaced with data.frame(x=,stringsAsFactors=FALSE)
- added 'Bug fixes' section to NEWS
Biobase
- Add a 'NEWS' file
- error message tweak for initialize,eSet-method
- BiobaseDevelopment.Rnw typo
'combine' on data.frame columns with mismatched levels causes a
warning, rather than error.
Biobase
fixed the English, as I will use this as an example in my book
several doc modifications were made
Biobase
several doc modifications were made
more cleaning out of exprSet stuff
updating man pages and removing references to exprSet
Biobase
Better manual page for combine,data.frame-method
Updating the license reference to reflect R standards.
Biobase
Allow ... of eSet[[i, ...]] <- value to contain varMetadata row information
Additional minor tidy related to documentation and error messages
Biobase
Earlier mention of minimalSet in the ExpressoinSetIntorudction.Rnw
Biobase
Minor doc tidy
more informative output when columns of data frames differ
Biobase
updating the CITATION
adding more authors to make the new standard of 10