Error in limma: Running multiple contrasts between groups

1

Hello everyone,

I am using limma-voom to run multiple contrasts with different groups at once but error happened.

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I have different groupings, including:

  1. 15 sets of AD_FC
  2. 18 sets of Healthy_FC
  3. 10 sets of AD_TC
  4. 19 sets of Healthy_TC
  5. 8 sets of AD_HI
  6. 10 sets of Healthy_HI

I used Single Count Matrix and two factors (1st factor - Condition, 2nd factor - Region) and 3 contrasts including (AD_FC-Healthy_FC), (AD_TC-Healthy_TC) and (AD_HI-Healthy_HI).

The cleaned dataset I used is as shown below (each column represents one set of data, except column 1):

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Is there any way to run limma to run contrasts according to different groupings, for example (AD_FC-Healthy_FC), (AD_TC-Healthy_TC) and (AD_HI-Healthy_HI)?