[BioC] Development of GCRMA-like methods

Rafael A. Irizarry ririzarr at jhsph.edu
Thu Feb 5 15:59:40 MET 2004

already done. its implemented in the latest version of gcrma (1.0.2) and 
described (not fully) in this paper:

Wu, Z and Irizarry, RA, Stochastic Models Inspired by Hybridization Theory 
for Short Oligonucleotide Arrays . Proceedings of RECOMB 2004 (to appear)

the reference you cite is outdated. we have been waiting (since July 
2003!) for referee reports from the journal of the american statistical 
association (JASA) to update it all in one go. apologies for this.


On Thu, 5 Feb 2004, Matthew Hannah wrote:

> Hi,
> I've been reading a few papers and I'm looking for some other opinions on a couple of questions/ideas I have. Basically this is directed towards a discussion on how methods such as GCRMA will develop.
> The main points of reference are - 
> (1) A model based BG adjustment for Oligo arrays. Wu, Irizarry et al.. 2003. Unpublished?
> (2) Solving the riddle of the bright MM's. Naef & Magnasco. 2003. Phys Rev E 68, 011906.
> My understanding is that-
> The first of these papers shows that MM intensity is related to GC content, and weights MM values towards the average distribution of the binding of MM with similar GC contents.
> The second proposes that most MM>PM occur because when the middle PM A/G is changed to MM T/C the smaller size of the substituted pyrimidine (C or T) allows room for the label on the target RNA (U or C) which would otherwise interfere with the binding to the PM.
> Are there plans to combine these ideas and would there be any benefit from doing so? Would sub-setting the MM based on both GC content and the middle base provide more accurate distributions to weight the MM's to? The majority of the MM>PM would have C (or T) as their middle base and 'averaging' them must surely distort things for the MM's with A or G?
> Finally Fig 3 in ref (2) shows nice fits of the positional effect due to having individual bases at different positions (1-25) in the PM probe. What would such fits look like for the MM probes, would it be similar or random/distorted due to non-specific binding? And would it help in answering why C has a smaller effect than G on intensity - or is this already known?
> Cheers
> Matt
> Dr. Matt Hannah
> Max-Planck Institute of Molecular Plant Physiology
> Am Mühlenburg 1
> 14476 Golm
> Germany
> + 49 (331) 567 8255 (phone)
> + 49 (331) 567 8250 (fax)
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