[CLOSED] Check edge construction from expression data

thpar / diffany

Diffany is an open-source toolbox for calculating and visualizing differential networks.

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Closed diffany-admin closed 9 years ago

diffany-admin commented 9 years ago

Issue by svlandeg Fri Oct 10 09:32:53 2014

Marieke: some incorrect edges?

e.g. EBF2 is induced, RAD51 (AT5G20850) in repressed -> why PPI increase? e.g. ARL (at2g44080) is up, AT4G15620 id down -> why PPI increase?

diffany-admin commented 9 years ago

Comment by svlandeg Mon Oct 13 15:53:31 2014

Findings Sofie:

RAD51 is not significantly repressed at 1.5h (0.02 logFC, and 1.00 FDR). Only significant down regulation at 24h (logFC -0.53 and FDR 0.03)
AT4G15620 has a negative fold change at all time points, but not significantly so @ 1.5h (0.99 FDR)

--> These edges are correct in the 1.5h network, at least according to the current (intended) implementation