Question: Network Analyzer in Cytoscape
0
gravatar for The Last Word
13 months ago by
The Last Word180
India
The Last Word180 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 • 628 views
ADD COMMENTlink modified 13 months ago by Jean-Karim Heriche21k • written 13 months ago by The Last Word180
1
gravatar for Jean-Karim Heriche
13 months ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche21k 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 13 months ago • written 13 months ago by Jean-Karim Heriche21k

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 13 months ago by The Last Word180

Yes this is the correlation coefficient.

ADD REPLYlink written 12 months ago by Jean-Karim Heriche21k
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