Hi all, I have a basic question regarding correlation calculation for gene micro array data. I have micro array data with gene names in rows and columns containing gene expression value. Now there are 2000 genes and 8 samples with 4 samples for healthy data and 4 samples for disease data. For correlation calculation among two genes should I have to consider only disease related 4 samples or should I consider all 8 samples at once and calculate correlation among genes. I want to use Matlab for correlation calculation but no idea which sample should I pick for this purpose. Also If there are more than two categories like healthy data 1, healthy data 2, disease data 1, disease data 1, then how should I continue with it. Thanks.
To find disease-specific modules, one approach would be to build two networks, one for healthy and one for disease then try and find the modules that differ between them. For this, you could use a tensor factorization approach based on the CP decomposition. For more details, see my tutorial on the topic.