Bioconductor Changelog

Bioconductor Changelog

	About Click here to learn more about this blog. Packages Click on a link for updates to that package only. Contam ExonMuncher Mvout PLM Para QCReport comp coretools io lmGUI pdnn Subscribe Subscribe to the Bioconductor Changlog.	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