Note: For Customer Support contact information, and for a link to the most up-to-date version of this help, please see Before You Begin.
ArrayStar is a powerful software tool for analyzing both global gene expression experiments and sequence variation tables across a panel of samples. For gene expression, ArrayStar handles data from oligonucleotide microarrays or spotted arrays and allows you to assess the quality of your data and define differentially expressed gene subsets using various statistical tests. ArrayStar also enables sequence quantification processing of Copy Number Variation (CNV), RNA-Seq, ChIP-Seq, and miRNA data.
Results are visualized interactively in high quality graphical displays and tabular views. ArrayStar allows you to undock and move views out of the main window so that you can have several views displayed on your screen simultaneously if desired. In addition, all views are interactive, so that subsets of genes selected in one view will be highlighted in all other views. This integrated approach can greatly facilitate mining your expression data in the most efficient way possible.
ArrayStar also allows you to customize graphical views by providing easy to use color and style settings, so that you can display your graph exactly as you want it. In addition, all graphical views can easily be copied and pasted into standard drawing programs, making the production of publication quality figures a simple task.
Microarray and sequence data can easily be imported into ArrayStar in a variety of file formats through the Project Setup Wizard. This wizard walks you through loading your files, normalizing your data, importing attributes and annotations, and setting up replicate sets. In addition, any arbitrary delimited text file containing microarray or sequence data can be imported into ArrayStar using the Data Import Wizard.
In cases where replicate datasets are available, they can be imported and grouped either in the Project Setup Wizard or in the Experiment List view as a replicate set (non-Variants workflows only). Subsequent analysis can be done using either the data averaged across replicates, or using individual experiments, as specified by you.
Additionally, multiple sequence lanes can be merged to create one “QSeq” experiment from multiple data files. QSeq is an “engine” in ArrayStar that enables sequence quantification processing of CNV, RNA-Seq, ChIP-Seq and miRNA data, as well as supporting SeqMan NGen .assembly and MID/multi-sample .assembly packages.
Multi-sample variation comparisons utilize SNP tables containing information on Single Nucleotide Polymorphisms (SNPs) and small insertions and deletions (indels). ArrayStar lets you import SNP tables directly from the SeqMan NGen assembler, use tables exported from SeqMan Pro, or import custom tables via a wizard.
To get started with ArrayStar, we suggest beginning with the topic 10 Steps for Using ArrayStar.