• marrayPlots

  • Referenced in 5 articles [sw08349]
  • Exploratory Analysis and Normalization of cDNA Microarray Data. This chapter describes a collection of four ... normalization of two-color cDNA microarray fluorescence intensity data. R’s object-oriented class/method mechanism ... tcltk widgets to automate data input and the creation of microarray-specific R objects ... storing these data. Functions for diagnostic plots of microarray spot statistics, such as boxplots, scatterplots...
  • minet

  • Referenced in 7 articles [sw08432]
  • tools for inferring transcriptional networks from microarray data. It is freely available from the Comprehensive...
  • MAANOVA

  • Referenced in 4 articles [sw08357]
  • describe a software package called MAANOVA (MicroArray ANalysis Of VAriance). MAANOVA is a collection ... analysis of gene expression data from two-color cDNA microarray experiments. It is available ... motivated by the need to analyze microarray data that arise from sophisticated designed experiments. MAANOVA ... rigorous statistical analysis of microarray data...
  • GOstats

  • Referenced in 6 articles [sw11312]
  • tools for interacting with GO and microarray data. A variety of basic manipulation tools...
  • PLASQ

  • Referenced in 6 articles [sw18746]
  • dosage in cancer cells from SNP array data. Human cancer is largely driven ... cells from single-nucleotide polymorphism (SNP) microarray data. Our approach is based upon a generalized...
  • MAPPFinder

  • Referenced in 6 articles [sw23711]
  • global gene-expression profile from microarray data. MAPPFinder is a tool that creates a global...
  • ofw

  • Referenced in 4 articles [sw10549]
  • tools exist for selecting variables in such data sets, especially when classes are numerous ... optimal feature weighting”. We focus on microarray data, although the method can be applied ... unbalanced multiclasses, a common characteristic in microarray data sets...
  • DNA

  • Referenced in 4 articles [sw26923]
  • framework for differential network analysis from microarray data. It has been long well known that ... quite some time. With the advent of microarray technology, newer computational techniques to detect such ... differential analysis of networks constructed from microarray data under two experimental settings. At the core...
  • GOSim

  • Referenced in 5 articles [sw08204]
  • high throughput data, such as DNA microarray data, researchers are capable of producing large amounts...
  • colcor

  • Referenced in 5 articles [sw12289]
  • correlation. Microarray experiments often yield a normal data matrix X whose rows correspond to genes ... mean-squared row correlation. Microarray data, however, frequently shows signs of column dependence. In this...
  • VarMixt

  • Referenced in 5 articles [sw21100]
  • differential analysis of replicated gene expression data. MOTIVATION: Identifying differentially regulated genes in experiments comparing ... often a key step in the microarray data analysis process. Many different approaches and methodological ... applied to both a ’two-colour’ cDNA microarray and an Affymetrix Genechip. Strong control...
  • LCE

  • Referenced in 5 articles [sw25277]
  • solves this problem by automatically combining multiple data partitions from different clusterings to improve both ... capability of the ensemble methodology for microarray data clustering. RESULTS: The link-based cluster ensemble...
  • Knorm

  • Referenced in 5 articles [sw16562]
  • involved in the underlying biological pathways. Microarray data from an increasing number of biologically interrelated...
  • PICNIC

  • Referenced in 6 articles [sw20386]
  • absolute allelic copy number variation with microarray cancer data. High-throughput oligonucleotide microarrays are commonly ... exemplified with affymetrix genome-wide SNP6.0 data from 755 cancer cell lines, enabling inference upon...
  • plsgenomics

  • Referenced in 3 articles [sw07949]
  • implements PLS methods for classification with microarray data and prediction of transcription factor activities from ... include two new classification methods for microarray data: GSIM and Ridge...
  • compHclust

  • Referenced in 3 articles [sw19128]
  • algorithms to cluster patient samples from microarray data, the clustering patterns generated by most algorithms ... given clustering. Finally, we analyze a microarray data set from 295 breast cancer patients, using...
  • ParaKMeans

  • Referenced in 4 articles [sw29731]
  • During the last decade, the use of microarrays to assess the transcriptome of many biological ... systems has generated an enormous amount of data. A common ... technique used to organize and analyze microarray data is to perform cluster analysis. While many ... genes from an experiment containing 200 microarrays can be quite time consuming and challenging...
  • EBarrays

  • Referenced in 31 articles [sw08355]
  • Microarrays. We have developed an empirical Bayes methodology for gene expression data to account...
  • INCLUSive

  • Referenced in 4 articles [sw17183]
  • portal and service registry for microarray and regulatory sequence analysis. INCLUSive is a suite ... tools for the analysis of gene expression data and the discovery of cis-regulatory sequence ... allow normalization, filtering and clustering of microarray data, functional scoring of gene clusters, sequence retrieval...
  • GSPPCA

  • Referenced in 4 articles [sw25977]
  • GSPPCA). Its usefulness is illustrated on synthetic data sets and on several real unsupervised feature ... genomics. In particular, using unlabeled microarray data, GSPPCA is shown to infer biologically relevant subsets...