Server Online Help

Getting Started

Installing Array Server

Install Array Server on Windows

Install Array Server on Linux

Concepts/Conventions

Data Organization

Project

• Distributed Project

• Simple Project

-Omic data

• Annotation

• Design

View

• Add View
• Float Current View
• CloseAllViews
• ShowSolutionExplorer
• ShowViewerController
• ShowDetailsWindow
• ManageViews
• Open Local View

Table

Rows

• SortRows
• Reorder Rows
• Reorders Rows By List
• Add Rows
• Group Rows
• Delete Rows
• Row Properties

Columns

• Sort Columns
• Reorder Columns
• Add Columns
• Combine Columns
• Paste Columns
• Delete Columns
• Column Properties
• Reorder Factor Levels
• Change Case
• Parse Column

MicroArray

Preprocess

• Filter
• Filter By Flags
• Normalize
• Impute
• Transform
• Combine
• Generate Ratios (Two-Color Array)
• Process Dye Swap (Two-Color Array)
• Remove Batch Effect

Summarize

• Summary Statistics
• Pariwise Correlation
• Missing Pattern
• Kernel Density
• Generate Contrast Data

QC

• Correlation-based QC
• Model-based Outllier Detection
• Principal Component Analysis
• QC Wizard

Inference

• General Linear Model
• Gene Set Enrichment Analysis
• Cox Model

Standard Tests

• One-way ANOVA
• Two-way ANOVA
• Two-way Nested ANOVA
• Trend Analysis

Other Tests

• One Group Test
• Two Group Test
• Paired Group Test
• Mutliple Group Test
• Proportion Data Logistic Regression Model
• Categorial Trait Association
• Two Group Permutation Test
• Multiple Probe Test
• Summarize Inference Report

Pattern

• Find Neighbors
• Correlate Covariate
• Spectral Map Analysis
• Hierarchiacal Clustering
• NMF Clustering
• Cluster Observations
• Cluster Variables
• Gene Shaving

Prediction

• Single Variable Classification
• Classification
• Predict Class
• Regression
• Predict Response

Annotation

• Molecular Signatures
• David
• Gene Ontology
• Upload UCSC Custom Track

Ingenuity

• Search
• View Canonical Pathway
• Create New Pathway
• Upload Data

R

• Run R Script (Microarray Data)