[BioC] GCRMA and background

[James W. MacDonald]

Amy Mikhail wrote:
> Dear list,
> 
> Was just following Richard's posts about GCRMA, and I'm curious to know
> why sequences would affect background - is it that some nucleotides have
> stronger binding affinities to dies than others or...?

No, it doesn't have anything to do with affinities to the dyes (in fact, 
Affy doesn't use a dye like cDNA arrays, but uses a fluophore called 
phycoerythrin). The affinities being modeled here are those between the 
target (fragmented cRNA) and probes (25-mers bound to the chip).

The basic idea is that the guanosine - cytidine binding is 'stronger' 
due to the fact that there are three hydrogen bonds as compared to two 
for adenosine - thymidine. However, as Zhijin noted, it is a bit more 
complicated than just GC content - it also has to do with where the 
guanosine and cytidine bases are located in the sequences as well.

Best,

Jim


> 
> Also is this mainly a problem for affy arrays or does it also affect
> spotted ones?
> 
> Cheers,
> Amy.
> 
> 
> 
>>-GCRMA assumes log normal distribution for background. It also assumes
>>that the parameters of that log normal distribution depends on the
>>probe sequence (a little more complicated than just GC content). Therefore
>>it uses "similar" probes to estimate those parameters. Which probes are
>>similar is determined by their sequences.
> 
> 
> 
> -------------------------------------------
> Amy Mikhail
> Research student
> University of Aberdeen
> Zoology Building
> Tillydrone Avenue
> Aberdeen AB24 2TZ
> Scotland
> Email: a.mikhail at abdn.ac.uk
> Phone: 00-44-1224-272880 (lab)
> 
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-- 
James W. MacDonald
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
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