I am running WGCNA on an expression matrix. I have recently transitioned from running the scripts on my work computer to a computing cluster, and with that transition have moved from testing the code on smaller datasets to the full data set. I have version controlled the package versions on both systems.
I have successfully completed the tutorials here: tutorials for WGCNA, main website with smaller data (I included almost half of the rows of my expression matrix ~40K out of ~100K rows). However when I try to scale to the full dataset, ~100K rows I get a non-critical error (the code doesn't crash, but I get a message) when calculating the Topological Overlap Matrix (TOM) with the command:
adjacency is the adjacency matrix from the
The code does not crash, but it prints to the console "
problem: *arbitrary number here* TOM entries are larger than 1", the number of entries that are larger than 1 only increases as I add more rows to the input expression matrix. I am quite confused because I am of the understanding that the values in the TOM matrix should be bounded between 0 and 1. Additionally, the script does not crash when I get the error. I also have been unable to find any other occurrences of people having this problem on the web, so I am very much at a loss as what to do.
Does anyone have any suggestions or advice on what I ought to do? I don't feel like I should continue with the analysis given the nature of the TOM definition, and I haven't been able to find any clues in the documentation for the function...
Thank you for your help!