My name is Mahes Muniandy and I am a doctoral student working on twin data. I have been using the WGCNA package to cluster and analyse my traits and gene expression data. Because I am using monozygotic twin data and would like to see how my twins cluster as pairs, I have taken the ratios of the values between the co-twins. In other words, I treat each pair as one sample and take twin1/twin2 to get the 'pair' values. Is this acceptable? Should I be taking delta value or doing something completely different? Incidently, I have also performed limma analysis on my expression data and I'm happy with that side of things.
Any ideas would be appreciated.
Obesity Research Unit,
University of Helsinki