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LIMMA Guide
LIMMA Guide: Quality Control and Statistical Analysis of Microarray Experiments Data
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OVERVIEW The LIMMA Guide is a plugin integrated in Spotfire DecisionSite© that implements a guided workflow to perform efficient and reliable analysis of two-channel microarray data. The LIMMA Guide is an integration of a wide range of powerful 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 QC & QA and get reliable lists of annotated differentially expressed genes. This new tool is fully customizable to specific needs like integration of existing R scripts. BENEFITS - Analytical Workflow: Enables non-expert users and those proficient in statistics to run full microarray analysis in a few minutes. - Powerful Statistics: 100% based on Bioconductor - Powerful Visualization: With Spotfire DecisionSite© (awarded as the best visualization tool on the microarray market) the user can create custom visualizations, clustering, reports among other features - Customizable and constantly evolving - Support for most-used scanner formats (GenePix, Scanalize,...) KEY FEATURES - Direct import from the most popular scanning devices (GenePix, Scanalize,...) - Interactive experiment design and visualization. - Quality control of replicates (Correlation Plot , CV versus Intensity Plot, Signal-to-Signal Correlation Plot and MA Plot) - Study of background signal values - Filtering methods like "Low quality data filtering" and Flags - Intra- and Inter-Array Normalization - Differential expression analysis with P-values, FDR (supported by R-Bioconductor) - Clustering algorithms (SOM, K-means, Hierarchical Clustering, PCA). - Reporting capabilities. - Automatic Gene Ontology (GO) and file-based annotation. - Customizable to new platforms or specific client needs. - Optionally integrated with KEGG database and Ingenuity PathwaysTM REQUIREMENTS - Spotfire DecisionSite© and Functional Genomics package - R environment - Bioconductor libraries LIMMA, Biobase and SAM For further functional analysis of large amounts of differentially expressed genes the output from LIMMA Guide can be directly integrated into the new analysis tool ArrayUnlockTM. For more information on ArrayUnlockTM, please check here
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| Integromics, S.L. |