Using WGCNA on Normalized Nanostring dataset

Question

[marion.ryan]

Hello, I am wondering how I could use the WGCNA package to explore a dataset derived from Nanostring (normalised), 486 detected targets, three time points (12 replicates in each). i.e. how could I prepare the data, all the tutorials are very much focused on RNASeq or microarray data.

Regards

Marion

[andres.firrincieli]

If properly normalized and log2 transformed WGCNA can be applied to different kind of data: amplicon sequencing, metabolomic, proteomic, abundance data from metagenomic sequencing. The tutorial will not change.

I would give it a try but I would not rely only on WGCNA.

Answer 1

[marion.ryan]

Thanks you so much for that, could you recommend alternatives to WGCNA? I am using cemitool also, but I'm just learning the rope with these and working my way through them.

[andres.firrincieli]

I can't recommend cemitool because I never used it. However, cemitool authors did a comparison whit WGCNA so you might want to take a look at the manuscript.