R News Volume 6/5

Articles published in the December 2006 issue of R News

Complete issue

Table of contents

Wolfgang Huber and Paul Murrell 1

Contributed Research Articles

Graphs and networks: Tools in Bioconductor
Li Long and Vince Carey 2

Modeling package dependencies using graphs
Seth Falcon 8

Image analysis for microscopy screens
Oleg Sklyar and Wolfgang Huber 12

Beadarray: An R package to analyse Illumina BeadArrays
Mark Dunning, Mike Smith, Natalie Thorne and Simon Tavaré 17

Transcript mapping with high-density tiling arrays
Matthew Ritchie and Wolfgang Huber 23

Analyzing flow cytometry data with Bioconductor
Nolwenn Le Meur and Florian Hahne 27

Protein complex membership estimation using apComplex
Denise Scholtens 32

SNP metadata access and use with Bioconductor
Vince Carey 36

Integrating biological data resources into R with biomaRt
Steffen Durinck 40

Identifying interesting genes with siggenes
Holger Schwender, Andreas Krause and Katja Ickstadt 45

Reverse engineering genetic networks using the GeneNet package
Juliane Schäfer, Rainer Opgen-Rhein and Korbinian Strimmer 50

A multivariate approach to integrating datasets using made4 and ade4
Aedín C. Culhane and Jean Thioulouse 54

Using amap and ctc packages for huge clustering
Antoine Lucas and Sylvain Jasson 58

Model-based microarray image analysis
Chris Fraley and Adrian E. Raftery 60

Sample size estimation for microarray experiments using the ssize package
Gregory R. Warnes 64