genotyping RLMM probe level model?
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@justin-borevitz-1002
Last seen 9.6 years ago
We'll we may give it a shot but there's always plenty of room for help.. thanks ----- Justin Borevitz http://naturalsystems.org/lab -----Original Message----- From: Ben Bolstad [mailto:bolstad@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 >
SNP probe RLMM SNP probe RLMM • 1.2k views
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@benilton-carvalho-1375
Last seen 4.0 years ago
Brazil/Campinas/UNICAMP
you also might want to take a look at CRLMM: http://www.bepress.com/jhubiostat/paper111/ b On Sep 20, 2006, at 11:25 PM, Justin Borevitz wrote: > We'll we may give it a shot but there's always plenty of room for > help.. > thanks > > ----- > 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 >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor
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Thanks Benilton! Terry sent me a copy a while back and just realizing how good this is for 2 allele 2 strand setup (for most SNPs this is plenty). Have you thought about allele specific expression (RNA), certainly a strand bias with low and saturating signal + length issues? Let me know if you are interested.. ----- Justin Borevitz http://naturalsystems.org/lab -----Original Message----- From: Benilton Carvalho [mailto:bcarvalh@jhsph.edu] Sent: Thursday, September 21, 2006 12:35 AM To: Justin Borevitz Cc: 'Ben Bolstad'; Bioconductor; 'Scott Smemo' Subject: Re: [BioC] genotyping RLMM probe level model? you also might want to take a look at CRLMM: http://www.bepress.com/jhubiostat/paper111/ b On Sep 20, 2006, at 11:25 PM, Justin Borevitz wrote: > We'll we may give it a shot but there's always plenty of room for > help.. > thanks > > ----- > 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 >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/ > gmane.science.biology.informatics.conductor
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