[BioC] LIMMA: choice of offset value for background correction method "normexp"

[Pie Muller]

Dear Bioconductors

I am using the package limma and understand that the type of background 
correction is important in the further processing of the data. Playing 
around with own data I found that using the "normexp" function with 
different values for the offset changes the final outcome of statistical 
testing. I am, therefore, a bit concerned about which is the best way to 
choose a value for the offset in "normexp". In the examples provided I 
found values of 25 or 50 but it was unclear to me why you would choose 
values in that range. Is there any rational in choosing a specific offset 
value other than just "playing around". In fact, what does the offset value 
mean? Offset from the background? Apologies if I didn't understand a simple 
principle here...

Thanks for any help on this issue!

Pie



_______________________________________________________

Dr Pie Mueller

Vector Research Division
Liverpool School of Tropical Medicine
Pembroke Place
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L3 5QA
UK

Tel. +44 (0)151 705 3123 (office)
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http://www.liv.ac.uk/lstm/