Bioconductor Changelog
   


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Thu, 02 Jul 2009

affycoretools
Added imports(AnnotationDbi, get) so things like get(goid, GOTERM) will work.

[/affycoretools] permanent link

Sun, 28 Jun 2009

affycoretools
Small fix to hyperGoutput. The output of annotation(GOHyperGResult) no longer contains the .db suffix, so this has to be added back on.

[/affycoretools] permanent link

Sat, 27 Jun 2009

affyPara
error in justvsnPara removed

[/affyPara] permanent link

Tue, 23 Jun 2009

affyPara
vignette update
build error removed
update for vigniette

[/affyPara] permanent link

Sat, 20 Jun 2009

affyPara
update for figures

[/affyPara] permanent link

Fri, 19 Jun 2009

affy
Fixed creation of .affyInternalEnv to ignore the functions designed to allow updating the AffyBatch methods. Previously we ended up with 'yBatch.methods' as one of the normalize.AffyBatch.methods or 'orrect.methods' as one of the pmcorrect.methods.

[/affy] permanent link

affyPara
new vignette createt
Update of Vigniette
vsn referencen added
update for correct address

[/affyPara] permanent link

Thu, 18 Jun 2009

affy
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.

[/affy] permanent link

Wed, 17 Jun 2009

affy
Replaced direct .Call(..., PACKAGE="affyio") with calls to R functions in affyio package where possible.
Minor typo corrections to customMethods vignette.
Minor typo corrections to buildinMethods vignette.
Minor typo corrections to vignette.
Edited man pages to remove typos and add missing words and punctuation.

[/affy] permanent link

affyio
Standardizing affyio R files during code review to understand new date information.

[/affyio] permanent link

Tue, 16 Jun 2009

affy
Fixed .Call("ReadHeader", ..., PACKAGE="affyio") calls to match signature in affyio.

[/affy] permanent link

Sat, 06 Jun 2009

affyio
(1.13.3) small fix to read.celfile.header() to deal with ScanDate
(1.13.2) Fix issues with CEL corruption not detected in read.probematrix

[/affyio] permanent link

Fri, 29 May 2009

affyPara
- additional tool to boxplotPara added: bagplot
- and qaSummary added

[/affyPara] permanent link

Thu, 28 May 2009

affyPara
read.affybatchPara added

[/affyPara] permanent link

Wed, 20 May 2009

affyio
(1.13.1) read.celfile.header(FILENAME,"full") returns an additional field "ScanDate"

[/affyio] permanent link

Thu, 30 Apr 2009

affyPara
mergeAffyBatch improved for memory amd time
mergeAffyBatch improved for memory amd time
error for multiprocessor machines fixed

[/affyPara] permanent link

Wed, 22 Apr 2009

affyContam
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.

[/affyContam] permanent link

affyio
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.

[/affyio] permanent link

affylmGUI
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.

[/affylmGUI] permanent link

affypdnn
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.

[/affypdnn] permanent link

Tue, 21 Apr 2009

affy
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.

[/affy] permanent link

affycoretools
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.

[/affycoretools] permanent link

affyPara
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.
small parameter update
small parameter update

[/affyPara] permanent link

affycomp
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.

[/affycomp] permanent link

affyPLM
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.

[/affyPLM] permanent link

affyQCReport
Bumped pkg versions for BioC 2.5 devel line.
Bumped pkg versions for BioC 2.4 release.

[/affyQCReport] permanent link

Thu, 16 Apr 2009

affy
Removed unneeded geneplotter dependency.

[/affy] permanent link

affyPLM
Removed geneplotter comment from vignette.
fix missing documentation warnings

[/affyPLM] permanent link

affyQCReport
Removed unneeded geneplotter dependency.

[/affyQCReport] permanent link

Wed, 15 Apr 2009

affyPLM
fix missing documentation warnings

[/affyPLM] permanent link

Wed, 25 Mar 2009

affyPara
Summarization optimized

[/affyPara] permanent link

Tue, 24 Mar 2009

affyPara
improvement for removeFiles
small improvement for distribute files
Option verbose set to getOption("verbose") and added . to names of internal functions

[/affyPara] permanent link

Sat, 21 Mar 2009

affyPara
Bug Fix in preproPara call

[/affyPara] permanent link

affyContam
Changed biocViews entry of Statistics to Bioinformatics.

[/affyContam] permanent link

affylmGUI
Changed biocViews entry of Statistics to Bioinformatics.

[/affylmGUI] permanent link

Fri, 20 Mar 2009

affyMvout
Changed biocViews entry of Statistics to Bioinformatics.

[/affyMvout] permanent link

Fri, 06 Mar 2009

affy
Rolled back r37752. Fixed affydata instead.
Fixed a cel file read issue related to the affydata package.

[/affy] permanent link

Sun, 22 Feb 2009

affy
explictly export methods on previously defined functions, so other
packages can importMethodsFrom(affy, ...)

[/affy] permanent link

Fri, 13 Feb 2009

affycoretools
Updated BiocViews.

[/affycoretools] permanent link

Thu, 12 Feb 2009

affycoretools
One more fix to account for changes to biomaRt.

[/affycoretools] permanent link