Introduction | What is a BufferedMatrix? | Accessing and Manipulating data stored within a BufferedMatrix | Functions for summarizing a BufferedMatrix | Applying your own function to the rows or columns of a BufferedMatrix | Elementwise transformation of BufferedMatrix objects | Converting between BufferedMatrix and Matrix objects | BufferedMatrix objects are pass-by reference | Future Enhancements

Introduction | Basic Usage of the MAplot function | Gaining greater control over the function | Advanced Usage | Special notes about differences in MAplot for AffyBatch, ExpressionSet and PLMset objects. | Final Comments

Introduction | Fitting Probe Level Models | How long will it take to run the model fitting procedures? | Dealing with the PLMset object | M-estimation: How fitPLM fits models | Variance Matrix and Standard error estimates for fitPLM

Introduction | Fitting Probe Level Models for Quality Assessment | Quality Diagnostics | Final Comments

Introduction | Using the threestep function | Methods available in threestep