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Bioconductor Changlog.
Tue, 13 Oct 2009
Biobase
Changed biocViews entry of Statistics to Bioinformatics.
Biobase
Add ScalarLogical
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
Fixed a typo in sampleNames replacement method.
Biobase
Bumping version numbers for BioC 2.4 devel.
Bumping version number in biocReposList to 2.4.
Bumping version numbers for BioC 2.3 release.
Biobase
several doc modifications were made
more cleaning out of exprSet stuff
updating man pages and removing references to exprSet
Biobase
some more trivial changes to rowQ error messages
some more trivial changes to rowQ error messages
trivial change to rowQ error message
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
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
added ... to the generic definition for description in order to be able to use it in the flowCore package
Biobase
warn when coercing types in combine,matrix,matrix
fixed a typo
use mode rather than typeof to check 'combine' matrix similarity
Biobase
Fixed trivial typo.
Biobase
Show correct varMetadata column names when labelDescription is in
a column other than the first
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
Added an extra annotation repository to biocReposList.
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
Bumping version number for repo in devel branch.
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
Biobase
fixed the English, as I will use this as an example in my book
several doc modifications were made
Biobase
updating the CITATION
adding more authors to make the new standard of 10
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
.buildBiobaseOpts() now fully respects user defined "BioC" option instead of overwriting parts of it
biocReposList() now gets the top URL from getOption("BioC") if defined. Bumped version to 2.3.2
Biobase
combine,eSet,eSet-method tries harder to produce up-to-date instances
from from outdated ones
Biobase
lcPrefixC wrote past end of Calloc'd memory
doc tidy
Biobase
checkClass unit test
Biobase
Minor doc tidy
more informative output when columns of data frames differ
Biobase
doc updates to conform to new Rd parser
Biobase
Fixed nrow call to ncol.
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
Fixed nrow call to ncol.
Biobase
futtzing with the print method for notes in an ExpressionSet - really
high yield work :-)
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
NEWS for makeDataPacakge
makeDataPackage gets a 'description' argument
sample.ExpressionSet abstract now claims correctly to be ExpressionSet
Biobase
Better manual page for combine,data.frame-method
Updating the license reference to reflect R standards.
Biobase
identical across channels
Biobase
Updating the NEWS file on the new scanDates slot in eSet.
Added scanDate slot to Biobase's eSet class, added functionality in affy to utilize the new scanDate slot and updated all the packages that create direct subclasses of eSet, ExpressionSet or NChannelSet.
Biobase
Allow ... of eSet[[i, ...]] <- value to contain varMetadata row information
Additional minor tidy related to documentation and error messages
Biobase
Force the S4 bit to be set during updateObject
- some adjustments to unit tests to access slots of very old instances
Biobase
correct usage in copySubsitute man page
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.