• impute

  • Referenced in 99 articles [sw14376]
  • microarrays. Motivation: Gene expression microarray experiments can generate data sets with multiple missing expression values ... investigate automated methods for estimating missing data. Results: We present a comparative study of several ... estimation of missing values in gene microarray data. We implemented and evaluated three methods ... tools for accurate estimation of missing microarray data under a variety of conditions. Availability...
  • limma

  • Referenced in 55 articles [sw10458]
  • limma: Linear Models for Microarray Data. A survey is given of differential expression analyses using...
  • boost

  • Referenced in 38 articles [sw35655]
  • tumor classification with gene expression data. Motivation: Microarray experiments are expected to contribute significantly ... boosting on real and simulated gene expression data. This quasi-guaranteed improvement can be obtained ... several established class prediction tools for microarray data. Availability: Software for the modified boosting algorithms ... studies and for the simulation of microarray data are available as an R package under...
  • vsn

  • Referenced in 29 articles [sw06105]
  • Variance stabilization and calibration for microarray data Bioconductor version: Release (2.10) The package implements ... estimator for the stochastic model of microarray data described in the references (see vignette...
  • ARACNE

  • Referenced in 36 articles [sw17200]
  • should enhance our ability to use microarray data to elucidate functional mechanisms that underlie cellular...
  • SparseLOGREG

  • Referenced in 27 articles [sw11449]
  • context of cancer diagnosis using microarray data. Results: The gene selection method suggested in this...
  • penalized

  • Referenced in 24 articles [sw06071]
  • cross-validation results for large data sets which is originally the most computationally demanding situation ... will be applied to several microarray data sets. An R package penalized, which implements...
  • TM4

  • Referenced in 12 articles [sw26846]
  • free, open-source system for microarray data management and analysis. Microarrays have emerged ... often challenged by the large quantities of data produced. Well-designed, user-friendly software ... capture, manage, and analyze effectively data from DNA microarray experiments. The TM4 suite ... tools consist of four major applications, Microarray Data Manager (MADAM), TIGR_Spotfinder, Microarray Data Analysis...
  • uniCox

  • Referenced in 14 articles [sw19131]
  • useful for high-dimensional data, including microarray data...
  • PAGE

  • Referenced in 7 articles [sw23828]
  • enrichment analysis (GSEA) is a microarray data analysis method that uses predefined gene sets ... identify significant biological changes in microarray data sets. GSEA is especially useful when gene expression ... changes in a given microarray data set is minimal or moderate. Results: We developed ... detect significantly changed gene sets from microarray data irrespective of different Affymetrix probe level analysis...
  • CLIFF

  • Referenced in 10 articles [sw35898]
  • CLIFF: clustering of high-dimensional microarray data via iterative feature filtering using normalized cuts ... clustering biological samples using gene expression microarray data. This clustering problem is difficult for several...
  • SVDMAN

  • Referenced in 8 articles [sw35896]
  • SVDMAN - singular value decomposition analysis of microarray data. .. Algorithms for the grouping method ... available in a software application called SVD Microarray ANalysis (SVDMAN). In addition to calculating ... provides a new means for using microarray data to develop hypotheses for gene associations...
  • GEOquery

  • Referenced in 9 articles [sw17285]
  • BioConductor. Microarray technology has become a standard molecular biology tool. Experimental data have been generated ... analysis and comprehension of genomic data. The tools contained in the BioConductor project represent many ... methods for the analysis of microarray and genomics data. We have developed a software tool ... Facilitating analyses and meta-analyses of microarray data will increase the efficiency with which biologically...
  • DNA

  • Referenced in 8 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...
  • edgeR

  • Referenced in 49 articles [sw06936]
  • data. t is expected that emerging digital gene expression (DGE) technologies will overtake microarray technologies ... functional genomics applications. One of the fundamental data analysis tasks, especially for gene expression studies...
  • BicAT

  • Referenced in 16 articles [sw12371]
  • exploration of the gene expression data, e.g. microarrays...
  • FABIA

  • Referenced in 10 articles [sw23382]
  • biclusters from true biclusters. On 100 simulated data sets with known true, artificially implanted biclusters ... competitors. FABIA was tested on microarray data sets which known, biological verfified subclusters and performed...
  • marrayClasses

  • Referenced in 7 articles [sw08346]
  • 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...
  • varSelRF

  • Referenced in 8 articles [sw08253]
  • applications in high-dimensional data (e.g., microarray data, and other genomics and proteomics applications...
  • superpc

  • Referenced in 8 articles [sw19130]
  • useful for high-dimnesional data, including microarray data. This function uses a form of cross...