Hi. I have some proteins data from TCPA (MD Anderson Cancer Center - http://app1.bioinformatics.mdanderson.org/tcpa/_design/basic/index.html).

I want to find PPI for these proteins in the literature for create a control matrix. I want to test  some network inference methods for these data sets and control the results with control matrix.  Is it possible or not with bioconductor packets?

İf yes, how do i?

Thanks a lot...

Hi. I did it with "ganet" r package. 

It allows performing globally assessing the inference performance of gene network inference algorithms over the available popular interaction databases.