This is the essential help guide and reference to the Bioconductor package for analysing high throughput biological data such as micro-arrays and more recently next generation sequencing.
The book was written in 2005 and so it reflects the state of the art then when Affymetrix dominated the microarray market. Now there are alternative suppliers, but the statistical assumptions and techniques for processing and normalisation largely remain the same as they have been derived from our experiences with Affymetrix. So it is slightly unfair for the negative review to say this is an advert for affy, now Bioconductor has modules to deal specifically with the Illumina bead arrays as well.
This book also does not cover next generation sequencing, as this was still in development when it was written and which is becoming an increasingly important use of Bioconductor. But in terms of understanding pipe-lining and the internal workings of Bioconductor you should get this book.
on 27 September 2007
granted, there is some useful info in this book, and if you can scratch through all of the affymetrix centric expositions you might be able to find it. There is much more to high throuput bioinformatics analysis than the proprietary apporaches of this large company. Gentleman's book does precious little even to acknowledge these. If you are stuck in the only interested in the myopic, and problematic affy world then I suppose you will like this book. If you are interested in a briader range of statistical analysis I would recomend looking elsewhere.