I'm trying to create a WGCNA network from Illumina microarray data for about 300 samples (multiple diseases from mouse, controls and cases). The data has been normalised using 75th Percentile Shift and only transcripts greater than 1.5 fold relative to the median across all samples have been retained. As a result, the matrix has negative values with a range of -12 to 12.
I've selected different matrices (top 5,000 or top 10,000 transcripts with highest variance) but my R.sq. values are really low (signed network) when I try soft thresholding and never really go higher than 0.4, even when I've set the powers all the way up to 70. Please see attached image. I've also tried unsigned network, and also tried taking absolute values from the matrix (so that the range is from 0 to 12), but nothing really makes any difference.
I'm a bit unsure of what the issue might be? Is it simply that there are too many samples and diseases and there aren't enough strong correlations in the matrix?
Thank you for any help.