[BioC] Average expression value from limma

[Ekta Jain]

Dear Bioconductor Mailing List,
I have a microarray data which i normalised using 'gcrma' followed by limma
for Mock vs Treated, 3 replicates in each group. The 'topTable' returns an
average expression value for each probeset. How is this exactly calculated?

Also i compared this with the average expression of each probeset for all
samples, such as
(Embedded image moved to file: pic17982.gif)

The 'Avg.Expr.from.limma' has a very high value as compared to the ones
obtained from the normalised data. Is there anything wrong?

Much appreciate any comments please.

Regards,
Ekta Jain
Research Analyst
Biotechnology and Bio-resources Division
The Energy and Resources Institute, India Habitat Centre
Lodhi Road, New Delhi - 110033
#09958818853
ekta.jain at teri.res.in


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