Diapositive 1

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Basic
or how to store your microArray experiments data
using BASE
CRS4, Bioinformatics Lab., S3D April 2007
Joel Masciocchi
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Basic
BASE is BioArray Software Environment a
comprehensive database server to manage
the massive amounts of data generated by
microarray experiments.
CRS4, Bioinformatics Lab., S3D, April 2007
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Basic
BASE is a free microarray database system. BASE
has been created and it is developed at the
University of Lund, in Sweden. It has a clean
and rather intuitive web interface. It offers a
natural work-flow for microarray experiments,
from microarray production to the analysis of
results.
CRS4, Bioinformatics Lab., S3D, April 2007
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The system is meant to be set up as a local
repository for a microarray laboratory's data,
eventually including raw images.
CRS4, Bioinformatics Lab., S3D, April 2007
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The administrator defines users and their
privileges (e.g. the right to enter samples),
and has full access to all data in the database.
Users can easily share their data with other
users through a system similar to the group/world
rights on Unix systems.
CRS4, Bioinformatics Lab., S3D, April 2007
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Basic
The analysis part of BASE revolves at the moment
around a plugin interface, where data is passed
in tab-separated files. This makes it a simple
task to get existing analysis tools work with
BASE (for example, there are plug-ins for using
the statistical language R).
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Basic

• Why BASE
• free
• nice web interface
• flexible system
• well suited for a lab
• dedicated team working on it
• good community contributions
• widely used
• improvement on the analysis side should be
  forthcoming

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Basic
Base differs from ArrayExpress. BASE is a much
lighter application, intended for distribution
and designed with LIMS type application for
pre-publication data. ArrayExpress is a big
application, designed to manage extremely large
amount of data and to function as public
repository.
CRS4, Bioinformatics Lab., S3D, April 2007
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How to use BASE Web Client
Interface Permissions Experiment Export data
CRS4, Bioinformatics Lab., S3D, April 2007
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Login Page

http//biobase.crs4.org8080/base
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Home Page

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Listing Page

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Experiment Listing Page

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View/Presets

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Column popup
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View Presets
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Permissions BASE is a multi-user environment
that supports cooperation between users while
protecting all data against unauthorized access
or modification.
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Basic
Projects Projects are an important part of the
permission system for several reasons 1 All
regular users may create a project, add items to
it and share it with other users. 2 All
items in a project are treated as one collection.
3 Items are automatically added to the
active project so there is almost no need to
share items manually. 4 Items shared
between projects

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Basic
The active project The active project concept is
central to the sharing system. The most
important reason is that new items will
automatically be included in the active project.
Without an active project you would have to
manually set the permission on all items you
create.
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Active Project or not ?
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Permissions for a Project
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Permissions for a Project(2)
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Permissions for a Project(3)
Members The permission level uses a one-letter
code as follows R Read U
Use W Write D Delete
O Take ownership P Set
permission
CRS4, Bioinformatics Lab., S3D, April 2007
Permission to change the owner of an item Take
ownership
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Basic
Experiment 1. Create a new Project 2.
Create raw Bioassays 3. Create a new
experiment 4. Analysing an experiment
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Create a Project
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Create a Project (2)
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Create a Project (3)
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Create a Project (4)
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Create a Project (5)
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Create a Project (6)
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Create a Project (7)
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Create a Project (8)
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Create a Project (9)
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Create a Raw BioAssay
you upload a Cell file with a Array design it's
called a Raw bioassay
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Array design You need to define the design of
the Affymetrix Chip in BASE, i.e. Import the
AffymetrixChip.cdf file. This step can only be
performed by a user with array LIMS
administrative privileges, an ordinary BASE user
does NOT have this privilege.
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Basic
CDF file
The chip definition file is a file generated by
Affymetrix The chip definition file contains all
the information needed to link each probe cell to
the gene or EST that it represents. Each probe
has a set of coordinates on the array
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Create a Raw BioAssay (2)
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Create a Raw BioAssay (3)
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Create a Raw BioAssay (3)
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Cel File

• A CEL file contains processed intensity values
  for each spot (after combining pixel level
  information).
• A CEL file is a quantitative summary of the
  scanned image.

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Create a Raw BioAssay (4)
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Create a Raw BioAssay (5)
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Create a Raw BioAssay (6)
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Create a Raw BioAssay (7)
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Create an Experiment
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Create an Experiment (2)
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Create an Experiment (3)
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Create an Experiment (4)
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Create an Experiment (5)
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Create a BioAssay set
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Create a BioAssay set (2)
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Create a BioAssay set (3)
The plug-in is required for Affymetrix data. The
plug-in will create a bioassay sets, to be able
to analyse the data in BASE. RMA is a Robust
Multichip Average. It consists of three steps a
background adjustment, a quantile normalization,
and finally summarization.
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Create a BioAssay set (4)
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Create a BioAssay set (5)
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Create a BioAssay set (6)
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Analyse Data
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Dot Plot
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Explorer of Results
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Export Data as mev File
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Export the DATA Before data from BASE database
can be used outside the program, it first had to
be exported to a file which then can be
downloaded to a local path from the BASE file
system.
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Export the DATA (2)
Mev is a versatile microarray data analysis
tool incorporates sophisticated algorithms
for clustering. visualizes the microarray
data. classifies the microarray
data. realizes statistical analysis of the
microarray data.
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Export the DATA (3)
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Export the DATA (4)
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BASE_at_CRS4 The server will be public on the 2th
of May Joel Masciocchi, Sergio Contrino, Michele
Muggiri, Patricia Rodriguez-Tome, Simone
Carcangiu, Frederic Reinier, Ricardo Medda,
Gianfranco Frau, Giuliana Brunetti, Elisabetta
Muscas.
CRS4, Bioinformatics Lab., S3D, April 2007