Gene network analysis

Question

[saj98]

Hello everyone

I am using cytoscape tool to analyse my RNA-seq data, I am using Kddn app. I have issue when I upload the condition #1 and condition#2 to run Kddn, it takes fore ever and did not come with the final screen to show the data. Does anyone have experience with this issue?

I really appreciate your time and help

Shaima

[Michael]

Hi Shaima, I don't have direct experience with this software but to help you, others will need at least the following additional info:

• what is the dimension of your data, size of your expression matrix
• are you only comparing two conditions at a time? do you have replicates
• forever is not exactly a precise category, so how long did you wait, how much memory did the process use? Maybe you can try it on a subset of the data, say 10% to estimate the timing.