Scale Free Topology Fit In Wgcna
I have analyzed this dataset (GSE26280) using NCBI GEOtoR . I wanted to perform WGCNA analysis on the differentially expressed genes. But the scale free topology fit is coming very different ( and also it starts from a -ve value). Is it because of the sample size ? I have taken 12 samples in this case. Any explanation for this graph would be really helpful.
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That's bizarre. Can you plot an image of the density of the similarity matrix?
I remember seeing similar "off" results when I accidentaly worked on the transposed expression matrix. If I remember correctly, WGNCA expect a samples * genes matrix, is this how your expression data is laid out?
No, my gene expression has always been genes*samples. I just pass the transpose around everywhere.