iDEP disconnects when selecting limma-voom or limma-trend methods for DEG1 tab with 2 Groups Demo Data

[JianYes]

Describe the bug When using the iDEP web application, I encounter a disconnection issue upon selecting either the limma-voom or limma-trend method within the DEG1 tab. This problem arises specifically when analyzing the provided 2 groups demo dataset. The application becomes unresponsive and loses connection, preventing further analysis. However, it works fine for other demo data files except 2 groups; Human, 2 groups; Mouse, and Big data; Human if the both factors are selected.

To Reproduce Steps to reproduce the behavior:

1. Load the 2 groups demo data in the iDEP interface.
2. Navigate to the DEG1 tab.
3. Select the method limma-voom or limma-trend and submit.
4. Observe that the application disconnects and becomes unresponsive.

Expected behavior The application should perform the differential expression analysis using the selected method without disconnection or loss of responsiveness.

Screenshots

[kamalmdmostafa]

I am encountering an issue with the Normalized data. Upon selecting the contrast pairs for comparison and hitting the submit button, the Shiny browser disconnects or closes.

[JianYes]

Would you please send an email to gelabinfo@gmail.com to explain the issue in detail? Thanks!

[gexijin]

I believed this is fixed. The reason is that when there are just two classes, limma returns results called logFC instead of log2FC.