I am trying to use the viper package and having trouble figuring out which regulatory network I should use. Should I build one with aracne-ap directly on my dataset or better to use one from another dataset?
I am working on a breast cancer dataset so my idea was to use viper with the regulatory networks defined in aracne.networks as they were built on TCGA so also cancer related (and even breast cancer related). I have the impression that the example in the vignette on Human B-cell used the same dataset (dset from the bcellViper package) to built the regulatory networks (regulon from the bcellViper package) but I am not 100% sure, does someone know if it's the case?
Thank you for your help!
> sessionInfo() R version 3.3.1 (2016-06-21) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.10.5 (Yosemite) locale:  en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages:  parallel stats graphics grDevices utils datasets methods base other attached packages:  aracne.networks_0.99.7 bcellViper_1.8.0 viper_1.7.4  Biobase_2.32.0 BiocGenerics_0.18.0 loaded via a namespace (and not attached):  MASS_7.3-45 class_7.3-14 tools_3.3.1 mixtools_1.0.4  KernSmooth_2.23-15 segmented_0.5-1.4 e1071_1.6-7 boot_1.3-18