This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - Oct. 31 2003: metaData - New versions of annotation data packages (except homology) are available for downloading. Mappings to RefSeq accession for a mRNA record (NM), mappings to RefSeq accession for a protein record (NP), and MIM number (OMIM) are included. Evidence code are included in GO mappings in XXXXLLMappings. JZ Oct 31 2003: Biobase - Removed the function setOptionPdfViewer(), as that functionality is no longer necessary. There is now a 'pdfviewer' option in R. Also modified openPDF to get the R option. JG

This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - Nov 07, 2003: Multiple Packages: Instances of 'apply(x,1,mean)', 'apply(x,2,mean') as well as the same for 'sum' were replaced with the faster 'rowMean', 'colMean' (and xxxSum). Packages affected: affycomp, affypdnn, affy, arrayMagic, daMA, gcrma, globaltest, gpls, marrayNorm, multtest, pamr, siggenes, and splicegear. JG Nov. 06, 2003: annotate: Function lookUp added. lookUp should be used to replace any get and multiget calls to get annotation data from data packages. For example, lookUp("9473672", "hgu95av2", "PMID") or lookUp(c("11706946", "10922468", "10634581"), "hgu95av2", "PMID") should be used istead of get("9473672", env = "hgu95av2PMID") or multiget(c("11706946", "10922468", "10634581"), env = "hgu95av2PMID"). JZ Nov 05 2003: AnnBuilder: Bug fixes for making annotation using LL id as the base map type. JZ Nov 05 2003: tkWidgets: eExplorer and pExplorer added to allow users to interactively explore R example code or contents of a given data package. JZ Nov 05 2003: limma 1.3.1. Bug fix for as.MAList. Slightly changed comments in install.R and aaa.R. GKS Nov 04 2003: reposTools - Fixed a bug where packages with a '.' in their name were not being registered as part of a repository. JG Nov 03 2003: CDF Packages - A package for the barley1 chip was contributed by Jim MacDonald. JG Nov 03 2003: DynDoc - removed the vignette() command as there is now a similar function in base that does basically the same thing. Also the function getVignetteKeyword has been added - this can be used to retrieve a metadata field from a vignette file (VignetteIndexEntry, VignetteDepends, etc). JG

This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - 15 Nov 2003: limma 1.3.3 - new function write.fit. GKS 11 Nov 2003: limma 1.3.2 - substantial upgrade to functions which identify and track control spots from the gene list including readTargets(), readSpotTypes(), controlStatus() and plotMA(). Routine edits to User's Guide. GKS

This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - Nov 21, 2003: ecolitk - Added annotation data from the GenProtEC website (MultiFun classification scheme mainly). Added plotting function 'linesChrom'. Added examples in the vignette. LG Nov 20, 2003: affy - ReadAffy()/read.affybatch() now offer preliminary support for the new binary CEL file format. Nov 20, 2003: externalVector - Put in function stubs for asinh(), acosh(), and atanh() which were not being exported in Win32 and thus the package would not compile. Now in Win32 these functions will report "unimplemented function". JG Nov. 18, 2003: AnnBuilder - all the parsers for parsing data from public data sources were moved from "data" to "scripts" directory. Vignetts and functions affected were modified accordingly. Users of AnnBuilder who wrote their own code rather than just use ABPkgBuilder should make sure that parsers provided by AnnBuilder be read from the "scripts" directory. JZ 18 Nov 2003: limma 1.3.4 - fix bug with exprSet object in lmFit(). GKS 16 Nov 2003: BioSeq1 - preparing S4 version, now really broken by intent. AJR

This is an automated message sent out weekly to report recent changes to Bioconductor packages. Please see the URL http://www.bioconductor.org/changelog.html for a complete history of changes. Unless otherwise noted, these changes apply to the developmental packages only. ---------------------------------------------------------------------- - 26 Nov 2003: All release 1.3 packages are now built against R-1.8.1 25 Nov 2003: webbioc - Several major changes. CS - Added function to automatically download all metadata packages - Modularized batch queueing system code for simpler extension - Added support for the Sun Grid Engine batch queueing system - E-mail notification now works universally and provides links - Temporarily switched just.rma() to rma() in affy module 24 Nov 2003: Added contributed package 'pickgene'. JG 22 Nov 2003 (??): affypdnn - bug fix (expressopdnn was returning the slot exprs instead of an object of class exprSet when some options were activated) 22 Nov 2003 (wh): prada 0.2.0 - checked in new package with tools for analysing and navigating data from high-throughput phenotyping ex- periments based on cellular assays and fluorescent detection (flow cytometry (FACS), high-content screening microscopy). Careful: the documentation is sketchy, a vignette does not yet exist, and the separation between features of general interest and ones that are lab- or experiment-specific is not yet clear.