Tutorials

Array Server/Viewer Tutorial

This tutorial is meant to get the user started accessing Array Server via Array Studio or Array Viewer. From searching "ratios" on the server, to retrieving fully analyzed GEO projects, this tutorial covers all the basics of the server.

SNP Data Analysis Tutorial

This tutorial is a great beginning guide to using Array Studio for SNP analysis. It includes a download link to a sample Illumina-Report formatted dataset, along with step-by-step directions for import of data, visualization of data, marker analysis, filtering of data, population structure (PCA), basic association analysis, categorical trait association analysis, quantitative trait association analysis, survival trait association analysis, and visualization of p-value results.

Affymetrix Data Analysis Tutorial

This tutorial is a great beginning guide to using Array Studio. It Includes a download link to sample Affymetrix dataset, along with step-by-step directions for MAS5 Quality Control Report, Chip Normalization, Principle Component Analysis, Hierarchical Clustering, Univariate Analysis, Gene Ontology Analysis, Pattern Matching, and the Audit Trail feature.

CNV Analysis Tutorial (CGH)

This tutorial is a great beginning guide to using Array Studio for CNV analysis. From importing the data, to generating segmentation results, to generating a number of CNV/CGH specific views (including Omicsoft's award winning Genome Browser (RegionView) and GenomeView for visualizing segmentation, Log2Ratios, and B-Allele Frequency.

ExonArray Data Analysis Tutorial

This tutorial is a great beginning guide to using Array Studio for ExonArray analysis. It includes importing your Affymetrix CEL files, ExonArray specific visualizations and Quality Control (PCA), Differential Expression at the probeset and exon level, as well as tests for alternative splicing..

Taqman Interactive Demonstration

This interactive demonstration allows the user to click their way through the importation of a Taqman dataset, using raw data from the ABI SDS software.

Click here to view in full screen mode

Click here to download the files (24kb) used in this interactive demo (SDS 2.1 Taqman file and Design Table) and try them out in Array Studio, just like in the demonstration.

Quick Guides

Solution Explorer Quick Guide

Explains the Solution Explorer, and is a great guide for new users to understand how to manage multiple projects, how to manage and compare lists, as well as some shortcuts in the Solution Explorer (for instance, right-clicking)

Importing Standard Illumina SNP data Quick Guide

Quick guide for importing SNP/Genotyping data using a standard Illumina Final Report

Importing Custom Array Illumina SNP data Quick Guide

Quick guide for importing Custom SNP/Genotyping data using a standard Illumina Final Report

Importing Illumina data for CNV Analysis Quick Guide

Quick guide for importing CNV data using a standard Illumina Final Report

Importing Affymetrix CEL files for CNV Analysis Quick Guide

Quick guide for importing CNV data using Affymetrix CEL files

Geo Data Import Quick Guide

Quick guide to importing datasets from the Gene Expression Omnibus, on the NCBI website. GEO is a public Gene Expression/Molecular Abundance repository, and more information can be found at http://www.ncbi.nlm.nih.gov/geo/. This tutorial demonstrates the ease in which a GEO dataset can be imported for further analysis and visualization in Array Studio.