Issues with DEG analysis


I’ve noticed that changes have been made to Express analyst for the “Statistical & Functional Analysis” for “A gene expression table”. When I normalize my RNAseq counts data (log 2 counts per million), I can no longer use use EdgeR for my comparisons of interest (i.e. “against a common control” or “pairewise”). Also, there’s an error message that appears even when I switch to Limma, and I’m unable to proceed to the dose response data…

How should I proceed?

Screen Shot 2023-04-17 at 2.31.41 PM

Hello, please follow our post guideline for detail trouble shooting.


Please see the data below for you to help me with my issue:

  1. Express analyst → DEG analysis

  2. Data uploaded
    S2fid_abundance_table_all_samples_submit_2_expressanalyst_trial 53.txt (2.4 MB)

  3. Document all steps leading to the issue.
    Step 1: Input: A gene expression table
    Step 2: Upload data (see screen shot)

Step 3: Data normalization (see screen shot)

Step 4: DEG analysis (see screen shot with error message)

How come, I can no longer use EdgeR (with normalized data) for DEG analysis? Also, when I use the suggested Limma for normalized data I get an error message…

The issue here is that your metadata are numbers. If you change to D0, D1, etc, it will work. We will add more checks so that ExpressAnalyst will warn you about this specific issue.