[BioC] question abour background subtraction in RMA

[James MacDonald]

Ad hoc is a latin term that literally means 'for this'. It means that
something is done either temporarily or only for a specific use. In this
case, I believe that it means the background estimation was temporary,
and would be improved in the future.

You can get an idea of how the parameters are estimated by viewing the
code for the functions bg.correct.rma, bg.adjust, and bg.parameters. The
actual code for RMA is written in C, so if you want to know exactly how
they are estimated you will have to look at that.

In addition, I believe Ben Bolstad has some manuscripts on his website
that have more details about the RMA background. Just google his name
and you can find it.

HTH,

Jim

 

James W. MacDonald
UMCCC Microarray Core Facility
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623

>>> "Antille,Nicolas,LAUSANNE,NRC-BAS"
<nicolas.antille at rdls.nestle.com> 06/13/03 07:34AM >>>
Hello!

I'm currently studying in details the Robust Multichip Average
procedure for
normalizing microarrays data. I am particulary intersted in the
background
subtraction. In the description of the affy package, it is said the
the
function bg.parameters provides adhoc estimates of the parameters of
the
normal and exponential distributions. What does the word adhoc means?
Can someone explain me the way these parameters are estimated?

Thanks in advance!

Regards

Nicolas

 
Nicolas Antille 
Statistician 
Nestlé Research Center 
PO Box 44, CH-1000 Lausanne 26 
Phone: + 41 21 785 9433 
<mailto:nicolas.antille at rdls.nestle.com>

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