Question: Network Analyzer in Cytoscape
0
gravatar for The Last Word
7 months ago by
The Last Word170
India
The Last Word170 wrote:

Hi,

Anyone who has used Cytoscape might be familiar with the Network Analyzer tool in Cytoscape which is used to calculate the degree distribution of the network. I did the same, plot the degree distribution and fit a power law y = ax(squared b) where b is the slope. Cytoscape gives the R-squared and correlation values of the network. By my understanding, The correlation coefficient (R) is squared to obtain the coefficient of determination (R-squared). However, none of my networks have the R-squared value as a square of the correlation value. For example, this is the correlation and R-squared values of three of my networks.

R-squared Correlation

0.684 0.963

0.532 0.942

0.621 0.949

Am I getting this wrong and does correlation mean something different and not correlation coefficient (R) in Cytoscape?

cytoscape • 386 views
ADD COMMENTlink modified 7 months ago by Jean-Karim Heriche18k • written 7 months ago by The Last Word170
1
gravatar for Jean-Karim Heriche
7 months ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche18k wrote:

If you're fitting a power law, the coefficient of determination is most likely calculated on log(data). This is probably mentioned somewhere in the docs.
EDIT: Found it mentioned in the docs here.

ADD COMMENTlink modified 7 months ago • written 7 months ago by Jean-Karim Heriche18k

Hi Jean, just to clarify, the correlation refers to the correlation coefficient right? It just says correlation and I am confused as to if that stands for something else.

ADD REPLYlink written 7 months ago by The Last Word170

Yes this is the correlation coefficient.

ADD REPLYlink written 6 months ago by Jean-Karim Heriche18k
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