[BioC] backgroundCorrect offset value

James W. MacDonald jmacdon at med.umich.edu
Fri Aug 26 22:48:43 CEST 2011

Hi Prasad,

On 8/26/2011 4:30 PM, Prasad Siddavatam wrote:
> Hi Jim,
> Thank you very much for you explanation. Now I can understand the reason.
> But when you said its up to the analyst to decide on the offset value.
> Is this statement based on the number of genes I am
> expecting (to be differentially expressed) or on some other criteria.

Yes ;-D.

Seriously though, this is where knowledge of the experiment, exploratory 
data analysis, etc come into play. You will likely have to make some 
assumptions, based on what your collaborators say about their 
expectations, what the data look like, etc.

It's not easy, and you never know if you made the correct assumptions. 
All you can do is realize what assumptions you have made, and have a 
reasonable rationale for why you made them.



> Its is very critical because I am using several types of
> arrays (agilent, cDNAs)
> Appreciate your help.
> Prasad
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James W. MacDonald, M.S.
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
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