# Presentation

# Web usage

# Data Management

# Data Preprocessing

# Expression Data Analysis

# Genomic Data Analysis

# Functional Profiling Analysis

Table of Contents

**MA-plots** are used to study dependences between the *log ratio* of **two** variables and the *mean values* of the same two variables. The **log ratios** of the two measurements are called **M** values (from “minus” in the log scale) and are represented in the **vertical** axis. The **mean values** of the two measurements are called **A** values (from “average” in the log scale) and are represented in the **horizontal** axis.

In microarray data contexts an MA-plot is used to compare *two channels of intensity measurements*. These two channels can be the **red** and **green** channels of one single chip of a two-color platform or the intensity measurements of two different arrays when using a single-channel platform. In a single-channel context at least two arrays are needed to draw a meaningful MA-plot.

Yang,Y.H., Dudoit,S., Luu,P., Lin,D.M., Peng,V., Ngai,J. and Speed,T.P. (2002) Normalization for CDNA microarray data: a robust composite method addressing single and multiple slide systhematic variation. Nucleic Acids Res., Vol.30, No.4, e15.

Bolstad, B. M., Irizarry, R. A., Astrand, M., Speed TP (2003). A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19, 185-193.