[BioC] genotyping RLMM probe level model?

[Justin Borevitz]

We'll we may give it a shot but there's always plenty of room for help..
thanks

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Justin Borevitz
http://naturalsystems.org/lab 


-----Original Message-----
From: Ben Bolstad [mailto:bolstad at stat.berkeley.edu] 
Sent: Wednesday, September 20, 2006 10:22 PM
To: Justin Borevitz
Cc: 'Scott Smemo'
Subject: RE: genotyping RLMM probe level model?

Oh, ok. Now I see where you are going. As far as I am aware no one is
doing that specifically. At one point I was thinking of expanding my PLM
work in that direction, but other things got in the way and it is very
very unlikely I'll ever get to it.

Best,

Ben


On Wed, 2006-09-20 at 22:12 -0500, Justin Borevitz wrote:
> Sorry, yes RLMM is like RMA to summarize probes prior to analysis eg
> Classify().  But what about analysis at the probe level? I'm developing
some
> SNP/tiling arrays, and we're adding 4 probes (2 alleles, 2 strands) for
each
> SNP and others for expression.  To score allele specific expression we'd
> look at the ratio (say of the two alleles), and we can do this with both
> strands.  With many samples each strand can predict a genotype, then the
two
> statistics combined rather than combine and create 1 statistic.
> 
> Thoughts? Someone must be doing this..
> Justin
>