Dr Guiyuan Lei
University of Newcastle
Newcastle upon Tyne, United Kingdom

Calibayes CISBAN

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System Biology

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The procedure for constructing decomposable Gaussian Graph from microarry data:

• Pre-process affymetrix microarray data using BioConductor

Use BioConductor to pre-process the affymetrix microarray data.

1. At the directory when you put your .CEL files, start R by type;

   R

2. Load the CDF library for hgu133plus2

   library("hgu133plus2cdf",lib.loc="/data/BioConductor/")

   Because the hgu133plus2cdf is not defaultly installed when install BioConductor, I install hgu133plus2cdf by hand. First download hgu133plus2cdf_1.43.tar.gz from website http://bioconductor.org/data/cdfenvs/repos/html/, store it in one directory. Go to this directory, use the following command to install the cdf library. "/data/BioConductor" is the directory where BioConductor is installed.

   R CMD INSTALL -l "/data/BioConductor" "hgu133plus2cdf_1.4.3.tar.gz"

3. library(affy)

4. senescent<-ReadAffy()

5. eset<-justRMA()

6. write.exprs(eset,file="mydata.txt")

• Select gene expression for sub gene list

Select gene expression by given gene IDs (the outfile of justRMA in BioConductor consists of gene IDs).

• Center the data to Standard Normal

Center the data to N(0,1), compg:~/GaussianModels/MH-d/pre_process_data/StandardNormalized.cpp

• Construct Gaussian Graphical models

1. Generate empty graph file empty.dat for specific number of genes;
2. Modifiy the data file and graph file, number of genes, number of samples and so on in the input file "infile";
3. In file metropolis.C, set the interval of iteration for recording output networks:

   if((k>2000000)&&(k%1000==0)){output graphs}

4. make metropolis

5. ./metropolis < infile > Young_networks.txt &

 

Last modified:
9 June, 2006