[BioC] WGCNA: help with comparing multiple GEO studies

Abhishek Pratap abhishek.vit at gmail.com
Sat Aug 23 01:39:50 CEST 2014

Hi Steve and Peter

My basic goal here is to study genetic similarities(if any) between a
group of GEO studies. I have downloaded about 6-8 studies and as one
would expect there is heterogeneity amongst them (diff platform,
versions, study sizes(15 - 120 samples) etc). After initial step of
normalization on each study I am trying to run a blockWiseConsensus
analysis to see shared modules amongst these different studies. I am
only using shared genes across all of the studies.

1. Wondering if doing consensus analysis across the studies is the
right approach here. Intuitively I dont think I want to build modules
on one study and compare with another as there are multiple studies
for comparison.

2.  Given varying samples sizes (15-120) I am not sure if I shud use a
very high soft power given 2 studies have < 20 samples or shud I
exclude these studies.

3. I have gone through tutorial II( Consensus analysis of female and
male liver expression data) but it is not clear to me that once the
network is built what are the different mechanisms in which one could
look at the consensus modules across different studies and run
functional enrichment analysis on them.


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