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)

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) > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623