April 2007 ACME Fixed chi-square calculation a bit to be actual counts in the cells rather than the counts of the marginals in a couple of cells. Fixed bug in write.sgr when colnames were not defined on vals affy Added 'cdf' argument to xy2indices() and indices2xy() so those without an AffyBatch can still map things. The cdf argument in this case is simply the name of the requisite cdf package. affycoretools Bugfix to vennSelect() when the number of probesets == 1 affyio Fixed issue with non-square cel file parsing using binary (xda) format cel files. The Affymetrix documentation is inconsistent with the reality (rows, cols swapped). annaffy Fixed GO links AnnBuilder Updated AnnBuilder to accommodate the changes to KEGG website. Added support for Bos taurus and fixed parsing routine for GENENAME annotate Fixed GO helper functions to deal with missing NA entries. Use sample.ExpressionSet data for Pretty Output vignette AnnotationDbi Changes to demo vignette to compare env and SQLite based annotation packages Add a revmap method for environment objects This allows revmap to be used on environment-based ann pkgs Added man pages for 'db_conn' and 'db_file' to HGU95AV2DB template beadarray Changed readBeadSummaryData to read BeadStudio V2 output CreateBeadSummaryData now assigns array names to the columns of the intensity data - 'pData' and 'phenoData' now defined for BeadLevelList - added 'targets' argument to qcPlots and updated man page bgx New Package: Bayesian integrated analysis of Affymetrix GeneChips Maintainer: Ernest Turro Biobase listLen now returns an integer vector (rather than numeric) and I also tried to better the documentation Further refinement of listLen In package code, INTEGER() is a function, so it is better to call it only once. Also improved the error message to give more information and added some detail to the man page. Add ScalarCharacter class This is a utility class that can be used to ease validation burden when writing classes that require a string slot. Add assayDataElement<- function Add readExpressionSet, deprecate read.exprSet, read.phenoData Changed welcome message biocGraph New Package: This package provides examples and code that make use of the different graph related packages produced by Bioconductor. Maintainer: Li Long biomaRt Fixed listAttributes function Removed array argument from getGene, getFeature and getGO as affymetrix arrays can now be specified using the type argument of these functions. Removed to.array and from.array arguments from getHomolog function as the affy arrays can be specified using the from.type and to.type arguments. To extend the possible types of identifiers that can be used for the getGene, getGO,etc functions, the value for the type argument has to be a filter given by the listFilters function. Updating handling of BooleanFilters. Whenever the user now uses a boolean filter a value of 1 or 0 will have to be specified to indicate true or false. To see if a filter is boolean the user can run listFilters with the showType argument = TRUE. Slimmed the listDatasets function, and it now returns a dataframe with character columns rather than factors Added specification of the web server port. Two new BioMarts don't use the default port 80 and were not accessible before this fix. Rewrote XML parsers to make code cleaner. Added detection of filter options. Some filters have a predetermed set of values and now these can be shown using the filterOptions function. Added the function filterType so users can determine the type of a filter (is important to know which filters are booleans). Updated vignette with the two new functions. Biostrings Replaced slots "start" (integer), "end" (integer) and "desc" (character) by single slot "views" (data frame with cols "start", "end" and "desc") in "BStringViews" class definition Added the matchProbePair() function Made matchProbePair() a new generic instead of a function. Default for 'baseOnly' arg in alphabetFrequency() is now FALSE instead of TRUE. Deprecated as.complex() in favor of toComplex() BufferedMatrix Changed median.polish.summarize.BufferedMatrix to median.polish.summarize Category Expose makeChrBandGraph. This patch also fixes the root node so that it does not contain all annotations. Add chrBandInciMat and makeChrBandInciMat functions Add geneIdsByCategory and doc Move sigCategories to Category and make it a generic Fix bug in hyperGTest for ChrMapHyperGParams objects R's intersect(x, y) function returns a vector with mode matching y if x and y have different modes. The bug was the result of assuming that standard coerce rules apply. They don't in this case as is documented in the intersect man page. cellHTS Fixed a bug in the read function (that didn't seem to have an effect in previous R versions), and made the verbose output a bit prettier copa Small change in copaPerm() that speeds the operation by about a gazillion-fold. Thanks to Laurent Gaultier for pointing this out. CORREP New Package: Multivariate correlation estimation and statistical inference. See package vignette. Maintainer: Dongxiao Zhu DNAcopy Added code to not split if maximal statistic is small (<= 0.1) and split if it is large (>= 7) without computing the p-values. Added warning that windowing code wil be deprecated in version 1.11 flowCore Updated Subset for new multiple filter options. Also fixed filterSummary Big changes to HowTo vignette. * Minor changes to coercion and read.flowSet to address Errol's troubles. * Removed as()<-. I guess Seth will be happy. * Minor documentation changes * A couple of small bugs with split * A $ accessor for flowSets GEOquery Updated GDS2eSet to return an object of class ExpressionSet instead of the old exprSet GOstats Fixup and document termGraph, inducedTermGraph, and plotGOTermGraph Fixed up the compGdist function a bit Modification to probeSetSummary() to allow end users the option of passing a vector of probeset IDs so the output of this function actually counts _all_ probesets that contributed to a significant GO term. graph Fix subGraph attribute handling for graphNEL This needs to be generalized for all subGraph methods. This patch adds proper handling of node and edge attributes for the subGraph operation. Before, we copied all attributes and now we only copy over the appropriate subset. Fix documentation of graphNEL class addEdge for graphNEL warns if edge already exists Note that for graphAM, this is an error. We warn when replacing an already existing edge using addEdge because in the past some users used graphNEL for representing non-simple graphs with multi-edges. Since this is no longer supported, a warning message is helpful. limma limma 2.9.17 - bug fix to read.maimages() for source="arrayvision". Now reads arrayvision files again for the first time since version 2.3.1. makecdfenv Modified make.cdf.packages() to create an additional environment with the usual package name appended with 'dim' (e.g., hgu95av2dim) that contains the chip dimensions. This is intended to be used by indices2xy() and xy2indices() in the affy package as a replacement for the deprecated xy2i() and i2xy() functions. Mfuzz Bug in mfuzz.plot2 fixed pcaMethods Added a svd method that is robust to outliers. Also a pca method based on this robust svd. Added vingette discussing handling of data with outliers nipals(center=T) was also accidentially sclaing the data, as we used scale(data, center=T). This has been fixed. svnImpute returned too many scores/loadings, this was fixed. And now we also assign correct row/column names to scores/loading matrices prada Fixed bug in drawGate when adding additional regions puma New Package: Most analyses of Affymetrix GeneChip data are based on point estimates of expression levels and ignore the uncertainty of such estimates. By propagating uncertainty to downstream analyses we can improve results from microarray analyses. For the first time, the puma package makes a suite of uncertainty propagation methods available to a general audience. puma also offers improvements in terms of scope and speed of execution over previously available uncertainty propagation methods. Included are summarisation, differential expression detection, clustering and PCA methods, together with useful plotting and data manipulation functions. Maintainer: Richard Pearson reb Added movt() - a moving t-test method for reb() Rgraphviz deprecate imageMap rename LLagopen to agopenSimple RWebServices Provide more informative error messages when Java -> R data tests go wrong Add indexNA in RComplex and RNumeric, and modify convert functions correspondingly. We tried to use NaN to represent both NaN and NA for R complex and R numberic vectors in Java. Now we seperate those two concepts. * change the java class name that represents all functions in a package from <package>.java to <package>Function.java siggenes EBAM updated, added new vignette Posterior probabilities are truncated at zero tilingArray Updated function segChrom and segmentation vignette xcms Modified findPeaks method: - Moved column "i" (peak number within combined EIC) to the second-to-last column - Added column "sn" with signal to noise ratio xcmsSets now include "i" and "sn" columns in the peaks matrix Added : - rawEIC method - findMZBoxes method - findPeaks.centWave method Modified findPeaks() method to support different findPeaks.* algorithms Added some lines concerning findPeaks.centWave to the vignette, changed output of centWave to matrix instead of data.frame Removed formerly deprecated function clustunique() Changed xcmsEIC plotting function from an S4 to an S3 method Removed all instances of isGeneric() ********************************************************** Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
[Bioc-devel] NEWS April 2007
1 message · James W. MacDonald