Dear all:
I have found quite the same question being asked at least twice but I still not have clear answer about how the ebayes method in LIMMA calculate the average expression value for a given experimental group.
I have used GCRMA to normalize my affimetrix values and then obtained the log2 expression values as (values below do not necessarily correspond to the same probe):

4395_CTL_LLA.CEL        :7.89
4404_CTL_LLA.CEL:        8.21
4413_CTL_LLA.CEL:       8.07
I have calculated by excel:
Simple mean = 8.055
Geometric mean = 8.054
Whereas the top table for average expression of these 3 values gave me: 8.055
This values are quite the same regardless of calculation method, However when more variability is among values the calculated average expression differs differs quite  largely:
4368_CTL_HLA.CEL:       8.26
4394_CTL_HLA.CEL:       7.17
4400_CTL_HLA.CEL:       8.70
Simple mean = 8.042
Geometric mean = 8.015
Whereas the top table for average expression of these 3 values gave me: 8.263. In this case this average expression value seems to be the median but on the next set of samples not.
4368_CTL_HLA.CEL:       10.758
4394_CTL_HLA.CEL:       10.907
4400_CTL_HLA.CEL:       7.634
Simple mean = 8.92
Geometric mean = 9.766
Whereas the top table for average expression of these 3 values gave me: 9.862, which in this case is not at all close to the median.

I will appreciate any help on this matter. It will also be appreciated, any additional though on whether the adjusted average expression (whichever the method is) is well enough to correct for expression variability within a given treatment, so I do not need to be worry for any potential outlier expression value or should I be concerned about?

Regards,
Miriam

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Miriam Garcia, MS, PhD
Department of Animal Sciences
University of Florida


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