CaArray
From Molecular WIKI
Contents |
About caArray
caArray is an open-source, web and programmatically accessible array data management system. caArray guides the annotation and exchange of array data using a federated model of local installations whose results are shareable across the cancer Biomedical Informatics Grid (caBIG™).
Introduction to caArray
- caArray Tool Summary Page (On caBIG™ Community Website)
- caArray project site
Example Use Cases for caArray
- Example use cases for caArray application.
caArray Monthly User Meetings
- caArray Monthly User Meetings is opened to everyone. Bring your question or suggest a new feature!
What is new
- Quick annoucement
- 2.2.0 is now available details
- What's new on caArray
Download caArray & Sample Data
caArray Documentation
| End User | Technical | Supplement |
|---|---|---|
caArray Knowledge Base
caArray FAQ
- caArray FAQ - Find the answers to the most frequently asked questions.
caArray Articles
- caArray Articles - caArray in depth: demo, articles and more.
caArray Case Studies
- caArray Case Studies - Still don't know if caArray is for you? Case studies will show you some examples of how caArray could be used in different scenarios.
caArray Success Stories
- caArray Success Stories - Each institution could have its own unique setting and requirement. Share your success or even not so successful story here. Your inputs will help others.
Questions and comments on caArray
Submit defects and feature requests on caArray
- Report a Defect or Request a Feature at caArray GForge Community Tracker
- Report a defect/feature request for caArray in Knowledge Center
- Report a Defect or Request a Feature at Bugzilla (not yet functional)
Open-source development
Integration with other tools
geWorkbench
geWorkbench can query for data in an instance of caArray via a Java API. Several operations are supported. You can:
- query for experiments, for example by platform or by species.
- select from which hybridizations in an experiment you wish to download data.
- download derived (summarized, probeset-level) data that has been parsed into the database. An example is the values loaded from Affymetrix CHP files (created through GCOS/MAS5). geWorkbench does not currently support retrieving or analyzing Affy CEL files directly.
The current release of geWorkbench, version 1.6.3, connects with caArray 2.2.0
The geWorkbench project page is at http://www.geworkbench.org.
The software can be downloaded from https://gforge.nci.nih.gov/frs/?group_id=78
GenePattern
GenePattern has a module that can retrieve data from caArray using its Java API. The CaArray2.0.1Importer lets you retrieve raw data files from caArray by experiment name or id. You can specify the extension of the data file that you want to download. The default is .CEL.
You can process CEL files using the GenePattern module ExpressionFileCreator. Once you have used ExpressionFileCreator, the data can be further analyzed using many different GenePattern analysis modules.
The CaArray2.0.1Importer module is compatible with caArray v2.0.1 and v2.0.2. You can download the CaArrayImporter here: https://gforge.nci.nih.gov/plugins/scmsvn/viewcvs.php/trunk/genepattern/cabig_ey2_2008/caArray20Importer/caArray2.0.1Importer.zip?root=genepattern&view=log
The CaArray2.1.0Importer module is compatible with caArray v2.1.x and v2.2.0. You can download the CaArrayImporter here: https://gforge.nci.nih.gov/plugins/scmsvn/viewcvs.php/trunk/genepattern/cabig_ey2_2008/caArrayImporter/caArray2.1.0Importer/caArray2.1.0Importer.zip?root=genepattern&view=log
You can download GenePattern here: http://www.genepattern.org
Once you've fetched your microarray data from caArray with the CaArray2.0.1Importer, you can do analysis on your data with the Replicated Affymetrix Maanova Analysis pipeline written at the Jackson Laboratory for GenePattern. This pipeline is available for download from the Jackson Laboratory's NCI Cancer Center caBIG page at: http://research.jax.org/cancer/download/index.html
Or directly from the download page: http://research.jax.org/cancer/download/registration.php
Once you fill-out the registration, you will download JAX_RepAffyMaanovaAnalysis.zip. You simply load this zip file to your GenePattern server via the option in the GenePattern menu for loading a zip file.
The pipeline consists of two modules JAX_AffyProcessing and JAX_AffyMaanova, and the pipeline itself JAX_RepAffyMaanovaAnalysis. The pipeline will run both of the modules for you you. This pipeline operates on the zip of CEL files generated by CaArray2.0.1Importer, and an experimental design file.
