<p>i got a similarity score matrix by using CCREPE package on R. I would like to visualize the co-occurence by using the app CoNet from Cytoscape. Everytime i upload the .TSV matrix and .TSV p-values, i got an error.</p>
<p>This is the similarity matrix:</p>
<p><a href="https://i.sstatic.net/UDOUkXrE.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/UDOUkXrE.png" alt="enter image description here" /></a></p>
<p>This is the p-value matrix:
<a href="https://i.sstatic.net/8M28xwoT.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/8M28xwoT.png" alt="enter image description here" /></a></p>
<p>This is how i upload the tho files in CoNet:
<a href="https://i.sstatic.net/TMTAE2FJ.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/TMTAE2FJ.png" alt="enter image description here" /></a></p>
<p>This is the error i get once i tap &quot;go&quot;:
<a href="https://i.sstatic.net/cbG1V4gY.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/cbG1V4gY.png" alt="enter image description here" /></a></p>

CC BY-SA 4.0
2024-07-26T16:38:36.057Z
Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Community
CC BY-SA 4.0
2024-07-26T22:02:48.330Z
Please show some of your input data. The first few lines of the .TSV matrix and .TSV p-values would be helpful.
gringer
CC BY-SA 4.0
2024-07-27T09:18:40.370Z
thanks for your reply. I posted more pictures
user21020
CC BY-SA 4.0
2024-08-01T03:55:43.473Z
My guess is that CoNet doesn't like NaN entries. Try changing those to 0 and see if it works.
Scooter Morris
<cytoscape>
How to visualize Similarity score matrix with CoNet app of Cytoscape
# How to visualize Similarity score matrix with CoNet app of Cytoscape

(Asked by: username_0 on 2024-07-26)

i got a similarity score matrix by using CCREPE package on R. I would like to visualize the co-occurence by using the app CoNet from Cytoscape. Everytime i upload the .TSV matrix and .TSV p-values, i got an error.

This is the similarity matrix:

[![enter image description here](https://i.sstatic.net/UDOUkXrE.png)](https://i.sstatic.net/UDOUkXrE.png)

This is the p-value matrix:
[![enter image description here](https://i.sstatic.net/8M28xwoT.png)](https://i.sstatic.net/8M28xwoT.png)

This is how i upload the tho files in CoNet:
[![enter image description here](https://i.sstatic.net/TMTAE2FJ.png)](https://i.sstatic.net/TMTAE2FJ.png)

This is the error i get once i tap "go":
[![enter image description here](https://i.sstatic.net/cbG1V4gY.png)](https://i.sstatic.net/cbG1V4gY.png)

**Tags:** cytoscape
> **Comments:**
> **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
> **username_2**: Please show some of your input data. The first few lines of the .TSV matrix and .TSV p-values would be helpful.  
> **username_0**: thanks for your reply. I posted more pictures  
> **username_3**: My guess is that CoNet doesn't like NaN entries. Try changing those to 0 and see if it works.  

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## 0 answers

