Note: as of 2009/03/10, changes that lead to different calculational results are marked as DIFF. 2009/11/22: 0.83 . new function modulePreservation calculates module preservation statistics between independent data sets . new dependence on package splines . new function labelPoints to semi-inteligently label points in a scatterplot. . extended functions pickSoftThreshold, pickHardThreshold . minor bugfix in scaleFreePlot . new function standardScreeningCensoredTime . new function scaleFreeFitIndex 2009/11/17: 0.82-1 . bugfix in plotEigengeneNetworks (thanks to Ronnie Alves for pointing it out) . bugfix in heatmapWithLegend when used with mixed color and text labels 2009/11/10: 0.82 . new function standardScreeningBinaryTrait . bugfix in verboseBarplot: the function now passes the ... arguments to barplot . verboseScatterplot gets argument sample for better handling of large vectors . labeledHeatmap gets arguments xColorWidth and yColorWidth that control the witdth of the color labels 2009/10/29: 0.81-2 . bugfix in blockwise[Consensus]Modules: function now works when number of modules exceeds number of available colors . bugfix in exportNetworkToCytoscape: all nodes are now included in the node file (thanks to Tim Gernat for pointing it out and suggesting the fix) 2009/10/22: 0.81-1 . addTraitToMEs now works with colnames instead of names . bugfix in bicor(x): when x has missing data, bicor now does not crash . minor bugfix in plotEigengeneNetworks: printAdjacency is now respected 2009/10/19: 0.81 . several functions from the now defunct package sma were added, mainly to allow our users to run all tutorials smoothly. Note that if sma package is used concurrently, identical copies of the duplicated functions will be available. Warning messages about this fact can be disregarded safely. . labeledHeatmap re-written to use an internal heatmapWithLegend function. This means labeledHeatmap now works also in complicated sectionings using layout(), which was not the case before. 2009/09/18: 0.80-1 . crash in blockwise[Consensus]Modules and TOM calculations when using bicor fixed; blockwise[Consensus]Modules and TOM calculations using compiled code get a new argument maxPOutliers corresponding to the bicor argument of the same name (see news in 0.80). 2009/09/13: 0.80 . new functions conformityBasedNetworkConcepts and fundamentalNetworkConcepts calculate network concepts (indices) . bicor gains the argument maxPOutliers specifying the maximum fraction of data that can be considered outliers . new function verboseBarplot to produce annotated barplots . verboseBarplot, verboseBoxplot and verboseScatterplot now have complete help files 2009/09/01: 0.79-4 . bug in networkConcepts fixed . goodGenesMS and goodSamplesMS now a bit more robust . new function vectorizeMatrix to turn a matrix into a vector of non-redundant components . orderMEs now works also on the single set output of moduleEigengenes. . plotColorUnderTree, plotDendroAndColors, and plotClusterTreeSamples are now capable of displaying text labels that identify the displayed colors by name. . overlapTable now works when the arguments are 1xn or nx1 matrices. 2009/08/07: 0.79-3 . GOenrichmentAnalysis now works for yeast data as well. Yeast GO mappings are given in a slightly different database (ORF identifiers instead of Entrez) and previous versions of the function did not handle this difference (thanks to Maryam Anwar for pointing this out). 2009/08/05: 0.79-2 . Default color in addGuideLines now darker ((grey30 instead of grey70). . Default color in addGrid now darker (grey30 instead of grey70). . Error in bicor help file corrected. . moduleEigengenes gets the option to turn off scaling expression data before calculating the singular value decomposition. This should only be used to speed up calculation if the data has been scaled previously. . Bugfix in simulateMultiExpr: the function now works when leaveOut=NULL . Minor changes to diagnostic messages in TOM calculations . Minor changes to printed values in verboseBoxplot . GOenrichmentAnalysis a bit more stable . GOenrichmentAnalysis can now analyze several sets of labels at the same time; the idea is to give the user the option to quickly calculate enrichments for a collection of competing module assignments. . Enrichment calculations can optionally be restricted to a subset of modules 2009/06/05: 0.79-1 . GOenrichmentAnalysis now faster and a bug in returned genePositions fixed. . function plotEigengeneNetworks gained two additional arguments controling the printing of numerical values into the adjacency heatmaps. 2009/06/01: 0.79 . Added (experimental) function GOenrichmentAnalysis for automatic GO enrichment analysis 2009/05/26: 0.78 . Package qvalue becomes optional. If it is not installed, q values will not be calculated in the network screening functions. 2009/05/18: 0.77-1 . Hubgene calculation in moduleEigengenes now works even if only one gene has valid data. . Bug in labeledBarplot fixed that crashed the function if no error bars were given. 2009/05/05: 0.77 . DIFF: reverting to default TOM denominator method "min" . Bug fix in .clustOrder affecting consensusOrderMEs and mergeCloseModules when there is only one proper module present. 2009/04/02: 0.76 . Display of p-value in verboseScatterplot improved: small p values now shown more accurately . Spurious warning message in matchLabels is now suppressed . additional TOM option added: use mean denominator instead of minimum . DIFF: default TOM denominator method is mean. Use TOMDenom = "min" where necessary to reproduce older results . help files for [unsigned]adjacency corrected 2009/03/18: 0.75 . fixed a bug in matchLabels that caused unrelated modules to be matched . faster correlation calculations are now implemented both for [bi]cor(x) as wellas [bi]cor(x,y). On platforms where POSIX threads are available, certain parts of the [bi]cor calculations are threaded . functions [bi]cor, blockwise[Consensus]Modules, TOMsimilarityFromExpr now have additional parameters providing control over threading and over the tradeoff between speed and precision in handling missing data in the correlation calculations . fixed a bug in bicor(x,y) that was present when any of the columns consisted of only missing data and that caused incorrect NAs and 0s in the result. . DIFF: softConnectivity now subtracts 1 from the sum of adjacencies to remove the adjacency of a gene with itself. . DIFF: order of parameters in softConnectivity has changed. . DIFF: default number of centers in [consensus]projectiveKMeans is now an attempt to fully utilize resources estimated from preferredSize. . softConnectivity now accepts parameter 'type' that can specify the network type to be used; . fixed a bug in function adjacency that would crash the function in certain circumstances. 2009/03/04: 0.73 . default p value threshold in matchLables relaxed to 5e-2 . DIFF: [consensus]ProjectiveKMeans now default to a much higher number since that seems to lead to better results. . Faster versions of correlation and bicorrelation implemented. Fast correlation available for general use in function cor1. . bugfix in labeledHeatmap: xLabels and xSymbols do not overlap anymore . goodGenes, goodGenesMS, etc now resistant to whole gene profiles containing only NAs . minor changes in verbosity of [consensus]projectiveKMeans 2009/02/18: 0.72 . corPvalueStudent now correctly returns small values instead of zero . minor changes in default sectioning in plotDendroAndColors . plotDendroAndColors and plotColorUnderTree now plot colors top to bottom (previously was bottom to top) . faster median calculation in C implementation of bicor . added function overlapTable for computing significance of module overlaps . added function matchLabels for relabeling modules in a source partition to best approximate module labels in a given reference partition 2009/02/06: 0.71-1 . minor changes in verbosity of TOM calculations . blockwise[Consensus]Modules: random seed is now set only if it is non-NULL; this allows the user to force the functions to run without setting a seed, which was not possible before. 2009/02/05: 0.71 . package flashClust that implements fast hierarchical clustering is now required and used throughut. 2009/01/29: 0.70 . adapted for dynamicTreeCut-1.20: PAM stage in the dynamic tree cut used in blockwise module detection functions can now optionally respect the dendrogram in the sense an object can be PAM-assigned only to clusters that lie below it on the branch that the object is merged into. Note that this requires dynamicTreeCut 1.20 or higher. . TOM calculation: "Rough guide to max array..." now respects verbose parameter 2009/01/25: 0.67-2 . bug in recutBlockwiseTrees fixed (only visible if some genes or samples were bad) . bug in clusterCoef fixed . typos in help files fixed (cutreeStatic[Color]) . drawing of color label rectangles slightly modified in labeledHeatmap to prevent excessively large rectangles 2008/12/23: 0.67-1 . help file for intramodularConnectivity corrected . corPvalueFisher corrected when twoSided=TRUE: used to give p-values inflated by a factor of 2 2008/12/09: 0.67 . addTraitToMEs now works also when the multiMEs only contain the eigengenes but no average expression . labeledBarplot now accepts xLabelsAngle . fixed interpretation of grey name in orderMEs, consensusOrderMEs . scaleTOMs in consensusBlockwiseModules now actually has an effect 2008/12/04: 0.66 . new function exportNetworkToCytoscape 2008/12/04: 0.65-3 . new function networkConcepts . Bug fix in plotEigengeneNetworks when only one set is given . Minor changes and cleanup in help files and printed diagnostics 2008/11/05: 0.65-2 . Bugfix in exportNetworkToVisANT: no more spurious errors when probe to gene name translation table is given. 2008/11/02: 0.65-1 . Bugfix in reassigning genes between modules when KME difference too significant: an empty set of reassign candidates doesn't throw an error anymore. . Several help files added 2008/10/25: 0.65 . added function preservationNetworkAdjacency 2008/10/09: 0.64 . different versions of package impute are now supported. . help files expanded . help files' syntax corrected so all item descriptions are now displayed properly. 2008/10/01: 0.63-1 . bug in [consensus]ProjectiveKMeans fixed that would cause a crash if the center with highest index became empty . numbers2colors resistant to values out of range of the given min and max. . p-value in verboseScaterplot now corresponds to the actual correlation printed instead of the Pearson correlation value. However, the p-values are always calculated assuming the correlation value is actually Pearson. 2008/09/18: 0.63 . [automaticN|n]etworkScreening now accept option getQValue that can be used to turn off q value calculations; they also report counts of module eigengenes with gene significances in specific intervals. 2008/09/17: 0.62-1 . C implementation of column quantile (i.e., apply(data, 2, quantile)) giving immense speedup of consensus quantile calculations in new function colQuantileC 2008/09/17: 0.62 . Fixed bugs in blockwiseConsensusModules when disk cache not in use, and when consensusQuantile>0 . Added function exportNetworkToVisANT to export a network to VisANT. . Help files for several functions added 2008/09/13: 0.61 . TOMdist function added, defined simply as 1-TOMsimilarity, for easier migration of older code. 2008/09/10: 0.60-3 . [consensus]projectiveKMeans now resistant to an svd failure, using a weighted mean if svd returns an error. 2008/09/05: 0.60-2 . Bug fix in C implementation of bicor (bad bug!!) 2008/09/04: 0.60-1 . Big fixes in blockwiseConsensusModules related to TOM sampling 2008/09/02: 0.60 . minCoreKME default now 0.5 (was 0.7 for Consensus functions, which didn't make much sense) . blockwise functions now complete all blocks even if there is a block with no modules detected or with an error during ME calculation. . consensusProjectiveKMeans can now optionally use mean as definition of consensus distance, improving convergence in multiple set situations . several help files added . bicor now implemented consistently in R code and in compiled code: both call the same set of C functions and treat NAs correctly and consistently. Functions bicov and bicorNAy are removed. . pickSoftThreshold now accepts networkType argument . blockwiseConsensusModules can now optionally save samples used for TOM scaling 2008/08/29: 0.55 . Changes of input arguments and output for blockwise[Consenus]Modules . Errors in pre-clustering and calculation of signed networks fixed . New functions for re-cutting dendrograms produced in blockwise[Consenus]Modules . Bug in the return value of blockwise[Consensus]Modules fixed: blockGenes now correctly refer to all genes instead of goodGenes; . New function numbers2colors 2008/08/26: 0.50-2 . Fixed bugs in blockwiseConsensusModules causing a crash when module eigengene calculation fails 2008/08/20: 0.50-1 . fixed bug in compiled code bicor1 function that used quick calculation whenever at least one of the x,y had the correct NAs instead of both. . fixed crash in consensusBlockwiseModules when data not checked for missing entries . added info printing when merging clusters in consensusProjectiveKMeans 2008/08/15: 0.50 . [consensus]projectiveKMeans improved: no crash when some clusters become empty, faster . blockwise[Consensus]Modules: additional parameter checkMissingData can optionally turn off checking for missing data when it's not necessary. . a few help files added 2008/08/05 . Added random seed setting to blockwise[Consensus]Modules and [consensus]ProjectiveKMeans for repeatability . Lowered reassignThreshold to 1e-6 to prevent too many reassigned genes. 2008/08/03: 0.42-2 . Fixed bug causing a crash when no modules are detected. 2008/08/02: 0.42-1 . More complete help pages, bug in blockwiseModules fixed (reported by Anatole Ghazalpour) 2008/07/23: 0.41 . Many enhancements, improvements and bugfixes 2008/06/02: . Changes to TOMplot to make the dendrograms on the side more informative . Changes to scaleFreePlot to pass more of ... to the plotting function (removed separate title() command). 2008/05/29: 0.12 . Performance improvements, extra parameters in blockwiseConsensusModules 2008/05/16: 0.11-1 . nearestNeighborConnectivity (and softConnectivity) now work even when there is 1 gene in the last block . More bug fixes. 2008/05/15: 0.11-0 . Numerous bug fixes . blockwise[Consensus]Modules fixed (ub-broken) from the change of batch to block. . blockwise[Consensus]Modules get an option to choose the TOM function. 0.1.0: Basic functions in place.