Question: Scale Free Topology Fit In Wgcna
gravatar for pixie@bioinfo
6.5 years ago by
pixie@bioinfo1.4k wrote:

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.

enter image description here

R network • 3.7k views
ADD COMMENTlink modified 6.5 years ago • written 6.5 years ago by pixie@bioinfo1.4k

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?

ADD REPLYlink written 6.4 years ago by Hayssam270

No, my gene expression has always been genes*samples. I just pass the transpose around everywhere.

ADD REPLYlink written 6.4 years ago by s.ritchie730

That's bizarre. Can you plot an image of the density of the similarity matrix?

ADD REPLYlink written 6.5 years ago by s.ritchie730
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