Hello lists,

I am using Bioconductor/Limma package to analyze microRNA arrays.
I have 7 replicate two-color arrays, 4 probe replicates each array. Follow Limma procedures, I had a list from topTable with LogFC(1) and other columns. In addition, I produced LogFC for each individual arrays from MAlist, the average LogFC(2) were then taken from 7 arrays to compare LogFC(1).

The LogFC(2) is similar to LogFC(1), for example 3.12 vs 3.2, but they're not exactly the same. 

My question is that why aren't these two columns of value the same? Did I calculate it mistakenly or something behind this during the Limma procedures?

Could anyone kindly explain it?

Thanks.

Kevin


      
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