Good evening, I am currently running a WGCNA analysis. As suggested by a colleague, I switched from regular single-block WGCNA calculation to blockwiseModules, due to large (42,000 genes) dataset size. By setting the max block dimension to 40,000 , I obtain two separate blocks. Also, TOM matrices are exported and saved separately.
I don’t know how to proceed at this point. The function produced some data objects, but also exported two separated TOMs matrices.
What should I do? Most of the downstream functions explicitly require to work on a TOM (exporting data to Cytoscape for instance). I can easily import the matrix back into R, but I have two of them (same as number of blocks). Do I need to merge them somehow? Or should work on the two matrices separately? If so, how is this done? The tutorial doesn’t really expand on this.
Thank you in advance!