[BioC] GCRMA and background

[Amy Mikhail]

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...?

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)