WGCNA filtering data input

Question

[adriana.gallego.02]

Hi, Im doing WGCNA analysis, im trying to filter and select genes to do the co-network expression, starting to do the adjencecy matrix I got this error, "Warning message: In max(d, na.rm = TRUE) : no non-missing arguments to max; returning -Inf" someone could tell me what that means? thanks

Answer 1

[mforde84]

Kindly, there's no way for us to determine what that error means without reproducible code.

Also, the documentation on WGCNA notes that you shouldn't filter most genes prior to network generation, otherwise you violate assumptions of the model. I think theres some leeway here for very lowly expressed genes e.g., with logCPM < 1 as they may generate more spurious correlations with other lowly expressed genes.