Fatima Sanchez Cabo, Zlatko Trajanoski, Kwang-Hyun Cho and Olaf Wolkenhauer
A Graphical Users Interface to Normalize Microarray Data
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Microarray technology is becoming an essential tool in functional genomics.
The possibility of monitoring the expression level of thousands of genes
simultaneously, as the response to a particular biological condition, gives
to the biologists the chance to widen the aims of their experiments and
opens a door to the understanding of cellular transcription processes. In
order to extract valuable information from the big amount of data that
microarrays experiments generate, suitable and powerful statistical and
computational methods are required. An example of the effort of statisticians
and computer scientists is the release of the first Bioconductor software
and the increasing number of functions for microarray data analysis implemented
in several programming languages (e.g. R, MATLAB, Java) by different research
teams all around the world.

In this paper, we describe a Graphical Users Interface (GUI) written in
MATLAB to deal with the normalization of microarray data. In our opinion,
not enough importance has been given yet either to the assessment of the
effect of the normalization on the data or to the study of the most suitable
normalization methods according to the experimental design. To aim these
objectives, a great variety of normalization methods were implemented in the
interface here described, allowing the user to visualize the data before and
after every step of the normalization process. Our interface suggests an
example of what should be done using also other softwares such as R.

The features implemented in this interface were validated using data sets
from microarray experiments carried out for Mycobacterium tuberculosis by the
Bacterial Microarray Group St.George's Hospital, Medical School in London and
for Streptomyces coelicolour by the Streptomyces group at UMIST.