Question: [DESeq2] Slight difference between lfcMLE and my calculated log2 fold change
gravatar for Mike
8 weeks ago by
Mike10 wrote:

The values I calculate manually for log2 fold change (using R or Excel) are always slightly different than the lfcMLE value, I'm curious why that would be (sorry, stats isn't my strong suit). For example (each condition has 3 replicates):

Condition 1 normalized counts: 18536.58274, 20600.98049, 22578.73105
Condition 2 normalized counts: 12705.48353, 8803.154338, 12085.95176

Condition 1 average: 20572.09809
Condition 2 average: 11198.19654

Calculated log2 fold change: log2(11198.19654/20572.09809) = -0.877422531
lfcMLE: -0.877250202

ADD COMMENTlink modified 8 weeks ago by Michael Love14k • written 8 weeks ago by Mike10
gravatar for Michael Love
8 weeks ago by
Michael Love14k
United States
Michael Love14k wrote:

There are slight modifications to the fitting procedure which make it more robust.

ADD COMMENTlink written 8 weeks ago by Michael Love14k
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