Manual for Chipster

Chipster is an analysis software for DNA microarray expression data. Most of the analysis tools have been implemented in R. We are also drawing on the ready-made annotation packages for commercially available chips. Currently Chipster works best with Affymetrix, Agilent and Illumina data. It is capable of importing also cDNA data, but since most of these do not have an annotation package in the Bioconductor repository, the functionality that requires annotation packages (for example annotation, pathway enrichment and and promoter analysis) is disabled.


Data import and preprocessing

Chipster is rather flexible in what type of data it can import. Data import and preprocessing have been described in more detail in these documents.

Tools

Every tool is decribed in detail on its own help page. The help page is divided into four parts: General description, Parameters, Details on how the tool works, and Output where the results are described. The Parameters part contains the list of parameters, their possible values (1-100) and their default values [10].

For developers

Chipster is an open source software that will be available for downloading from Sourceforge. The Wiki in Sourceforge provides developers with extra information regarding a local installation and configuring and strating the system:

Copyright