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Category Genomics>Gene Expression Analysis/Profiling/Tools Abstract Integromics LIMMA Guide is an interactive analytical tool for quality control and statistical analysis of microarray data. The LIMMA Guide is a plugin integrated in Spotfire DecisionSite (see G6G Product Number 20061) that implements a guided workflow to perform efficient and reliable analysis of two-channel microarray data. The LIMMA (see Note 1) Guide is an integration of a wide range of advanced statistical libraries of Bioconductor. Therefore, the end user benefits from the combination of the best available tools for statistical analysis (R- Bioconductor) and visual data mining (Spotfire). After automatically importing the raw intensity data, researchers can perform advanced Quality Control (QC) and Quality Assurance (QA) and receive reliable lists of annotated differentially expressed genes. This tool is fully customizable to specific needs such as, the integration of existing R scripts.
1) Support for multiple scanner formats -- Direct importing from the most popular scanning devices via scanner files from Agilent, GenePix, Scanalize, etc. 2) Validate your results with state-of-the-art statistics -- Quality control of replicates, filtering methods, study of background signal values, normalization, differential expression analysis supported by Bioconductor’s algorithms. 3) Advanced interactive visualization in Spotfire DecisionSite -- Users can benefit from unique capabilities by browsing and inspecting gene expression data in Spotfire as well as other outstanding features such as, clustering methods, report generation and gene ontology (GO) integration. 4) Differential expression analysis -- P-value and False Discovery Rate (FDR) correction methods supported by Bioconductor. 5) Quality control of replicates -- via Correlation Plot, Coefficient of Variation (CV) versus Intensity Plot, Signal-to-Signal Correlation Plot and MA Plot. 6) Offers filtering methods -- such as, "Low quality data filtering" and Flags. 7) Clustering algorithms offered -- Self Organizing Map (SOM), K- means, Hierarchical Clustering, and Principal Component Analysis (PCA). 8) Provides automatic Gene Ontology (GO) and file-based annotation. 9) Offers optional integration with the KEGG database and Ingenuity Pathways (see G6G Product Number 20017). Software requirements -- 1) Spotfire DecisionSite and Functional Genomics package. 2) The R environment. 3) Bioconductor libraries LIMMA, Biobase and SAM (see G6G Product Number 20066). Note 1: Linear Models for Microarray Data (LIMMA) -- A software package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression. The package includes pre- processing capabilities for two-color spotted arrays. The differential expression methods apply to all array platforms and treat Affymetrix, single channel and two channel experiments in a unified way. Note 2: For further functional analysis of large amounts of differentially expressed genes that output from the LIMMA Guide, you can directly integrate this data into the advanced analysis tool ArrayUnlock (see G6G Product Number 20102). System Requirements Contact manufacturer Manufacturer Home office; see web site for international locations.
Centro Nacional de Biotecnología - CNB C/ Darwin 3 28049 Cantoblanco Madrid, Spain Phone: (+34) 91 585 5305 Fax: (+34) 91 585 5315 e-mail: technical.support@integromics.com
Price Contact manufacturer G6G Product Number 20101 G6G Manufacturer Number 101520 |
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