Strategies for aggregating gene expression data:

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

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Please send your suggestions and comments to: shorvath@mednet.ucla.edu