CAPweb (Copy number Array analysis Platform on the web)
A web-based platform for Copy number microarray management and analysis.

Version: 2.3

CAPweb tutorial


CAPweb is a user-friendly interface to store, analyze and visualize copy number microarray data.
CAPweb starts after image analysis (a gpr file for example) and goes up to the biological results. Different input format are supported:
Maia -  Genepix -  Spot -  Imagen -  Agilent -  Affymetrix SNP 100k/500k


DOCUMENTATION PDF
Analysis Parameters click here
VAMP click here

Register, Upload and manage your project

The user fills the registration form in and receives an email with the login and the password.
The login and password are display in the home page.
The user can create one or more project by giving a name. At this step the user can upload his own files.
The user uploads the result of CGH-array image analysis files (here agilent format). The user can download the demo file to see the CAPweb pipeline. There is also an image of expected raw data file.
Once uploaded, the user has access to some information about his file:
The user can upload other files or come back to the project home page.
When the user clicks on CAP, a new window opens to start the analysis. The CAPweb chip page is always open.

Launch the Analysis

There are 2 parameters:
Advised users can modify MANOR and GLAD parameters. Here is a list of these parameters :
The user may check or change the parameters before launching the CAPweb pipeline.
When the analysis is running, the user may upload another file or launch another analysis.
If the user accidently closes the analysis window before the end, normalization and breakpoints detection keep working in background. There is no need to restart the analysis. Once the analysis will be completed, the corresponding summary report will appear on the CAPweb array page.

Summary report and VAMP    

The summary report is a crucial step in the CAPweb pipeline. The user decides to keep or to discard the analysis. The user can also export the raw data and the analysed data.
The export spot-level data format is the excel format.
The export clone-level data format is the excel format.
The user can delete the analysis and can restart the same analysis with other parameters.
The user can integrate the analysis in the VAMP software. VAMP requires the Java 1.4.2 plugin.
To download the plugin for windows click here


Patient Number / Clinical and Transcriptome Data

The user creates one or several Patient Number   
At this step the use can associate the Patient Number with an analyzed array   
(the user can associate a patient number when launching the analysis)
The user uploads a clinical data file and associate the file with a patient number   
There is also an image of expected clinical data file.
The use can modify directly the clinical data file (update button).
The file is display in the web page and the user can add or delete some clinical data   
The user uploads a transcriptome data file, give a name and associate the file with a patient number   
There is also an image of expected transcriptome data file.



CAPweb and VAMP are accessible at http://bioinfo-out.curie.fr/CAPweb and http://bioinfo-out.curie.fr/vamp.
Contact : bioinfo | Bioinformatics Home Page : http://bioinfo.curie.fr | Institut Curie Home Page : http://www.curie.fr