Hi,

I am using edgeR for a 2x2 factorial design (Strain*Treatment) without any replicates and the estimateGLMCommonDisp and glmFit functions.

When I run estimateGLMCommonDisp, I get warnings
1: In optimize(f = fun, interval = interval^0.25, y = y,  ... :
  NA/Inf replaced by maximum positive value
and when I run glmFit and then glmLRT, I get huge fold change values for some genes.

However, if I do a pairwise exactTest for the samples examined for the above contrast, the fold change for that genes is high but normal.

I would really appreciate any feedback on the cause of warnings and huge logFC.

Many thanks for your help.

Best,
Ioannis

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