Question: Integrated genomic analysis - mRNA, proteomics, flow, miRNA-seq
gravatar for chris86
2.8 years ago by
UCL, United Kingdom
chris86380 wrote:


We have a big patient cohort and are wondering on the best ways to integrate the data. So far we have been using WGCNA on the microarray data with moderate success, but the question is how to we approach this when multiple genomic platforms must all be integrated? So we are interested in clustering the data using the platforms together with respect to clinical data (consensus clustering, iclusterplus), then also prediction of prognosis, and also network construction/ module generation with correlations to clinical data (WGCNA, ARACNE). Does anyone have any advice here? Any neat packages I am missing?

Kind thanks,



ADD COMMENTlink modified 2.8 years ago by Levi Waldron790 • written 2.8 years ago by chris86380
gravatar for Levi Waldron
2.8 years ago by
Levi Waldron790
CUNY Graduate School of Public Health and Health Policy, New York, NY
Levi Waldron790 wrote:

Hi Chris,

the section "Tools for integrative genomic data analysis" and Table 4 in survey some more tools you might be interested in. 

Also, we have a working prototype of a data class for data management of this kind of study (, built vignette at It doesn't implement high-level methods like the ones you mention, but rather helps make sure your samples are aligned correctly and helps to do things like subset or intersect by genes or whatever features.  If you want to try it out, I'd be happy to help. 



ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by Levi Waldron790

Thanks I am taking a look at these.

ADD REPLYlink written 2.8 years ago by chris86380
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