Insightful Miner™ Application Deployment of S+ArrayAnalyzer®

S+ArrayAnalyzer functionality is readily deployed through the Insightful Miner data mining workbench. S+ArrayMiner provides a structured and guided analysis of microarray data. The solution is based on the Insightful S-PLUS® statistics and graphics engine and the Insightful Miner data mining workbench.

The S+ArrayMiner solution provides:

Guided Work Flow: the iconic pipeline user interface leads you through the complete microarray analysis process, step by step.

Easy data access: The interface leads you through data access/upload, exploratory data analysis and normalization in order to prepare your data for analysis. Import of Affymetrix data including cel/cdf/chp files and MAS4/MAS5 summaries is straightforward. Connection to Affymetrix LIMS and APIs is also accommodated. For cDNA data, importing of several file formats, e.g. GenePix and Spot, is readily accomplished.

Leading Statistical Methods: ArrayAnalyzer provides cutting-edge statistical methodology for microarray analysis. By working in collaboration with the leading researchers in the field, and incorporating methods from the open-source Bioconductor project and from our own research collaborations with leading universities, we've been able to provide a comprehensive suite of methods for microarray analysis including:

Normalization Methods:

• Median and inter-quartile range
• Quantiles with robust option
• Local and cubic spline regression
• 2-D local regression and within-printtip methods for cDNA arrays

Differential Expression Tests:

• Two sample and paired t-test
• One-way ANOVA methods
• Wilcoxon test
• Local pooled error tests

FWER control

• Bonferroni
• Hochberg (1988)
• Holm (1979)
• Westfall & Young (1993)

FDR control

• Benjamini and Hochberg (1995)
• Benjamini and Yekutieli (2001)

Interactive Visual Annotation and Tabular/Graphical Reports
S+ArrayAnalyzer produces interactive tabular and graphical summaries of differentially expressed genes resulting from a variety of available differential expression analyses. These results are linked to public and proprietary databases for rapid identification and annotation of differentially expressed genes.S+ArrayAnalyzer's interactive reports (e.g. graphlets) can easily be shared across the Web with other colleagues, even if they don't have S+ArrayAnalyzer.

Interactive Visual Annotation and Reports include:

• pre-and post- normalization plots
• interactive volcano plot of differential expression
• variance function plots
• whole genome plots
• heat maps
• cluster analysis plots

These all include interactive hyperlinks to Unigene, LocusLink, PubMed, GenBank, AmiGO and other online or internal databases [see a demo of interactive reporting with ArrayAnalyzer]

An open and extensible environment, to stay abreast of the latest advancements in bioinformatics
Because S+ArrayAnalyzer is integrated with the award-winning S-PLUS® data analysis environment, it can adapt to the rapidly-changing world of microarray analysis. Instead of being locked in to black-box algorithms, S+ArrayAnalyzer's algorithms are highly extendable. And by using the ACM-award-winning S programming language- including a suite of object-oriented tools provided