Dear list,
  I have another question regarding using Limma.  I have multiple groups in my experiments and I would like to read them all to limma even though I only compare two of them, since I believe the moderated t-test will give me a better result with more data.  However, when we did more replicates for two of the groups that I am not comparing, I found that at lease one of the important genes is not in the final list using BH-adjust p-value of 0.01 as the cutoff.  I checked the data and found in one of the groups the variation in expression value among samples is big and thus affected the BH-adjusted P.  What should I do?  Just use the data of the related two groups for consistent result or use all the availabe data (different results when add more experiments)?
  Thanks for your suggestions!
  Lisa

 		
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