The collapseRows R function
JA Miller, C Cai, P Langfelder, DH Geschwind, SM Kurian, DR Salomon, S Horvath
Email Addresses
General questions: jeremyinla@gmail.com Statistical correspondence: shorvath@mednet.ucla.edu
ABSTRACT
This web site includes data and statistical code for the paper:
* JA Miller, C Cai, P Langfelder, DH Geschwind, SM Kurian, DR Salomon, S Horvath (2011)
Strategies for aggregating gene expression data: The collapseRows R function.
BMC Bioinformatics (submitted).
Link to paper: (not yet available)
Contents Real Data Analysis R-code for performing analysis in paper
Code document (.doc): contains word version (recommended for Mac users).
Code document (.pdf): contains pdf version (recommended for PC users).
Download the following R function files, which contain several R functions needed for the analysis. collapseRows function: you should not need this if the latest version of WGCNA is installed collapseRows help file: you should not need this if the latest version of WGCNA is installed Network R Functions
Other necessary functions for analysis
Microarray data in proper format
Data sets (zipped): (LARGE: 391 MB). Unzip in your R working directory. Data files are explained in code document.
Other material regarding weighted gene co-expression network analysis
Weighted Gene Co-Expression Network Page
The weighted gene co-expression network analysis method is described in Theory Paper 1: Zhang and Horvath (2005)
For a more mathematical description of weighted gene co-expression networks, see: Dong and Horvath (2007, 2008)
2011-05-20
Please send your suggestions and comments to: shorvath@mednet.ucla.edu