User: Justin Borevitz

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Posts by Justin Borevitz

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what is the best way to correlate SFP data to a phylogenetic correlation? (fwd)
... Hi, great question and a powerful approach. My first thought is to consider the traits separately, # of hosts and virulence. Then consider SFP haplotypes throughout the genome in sliding windows, but blocks would be preferred. You need to associate a plasmodium haplotypes with the quantitative trai ...
written 12.1 years ago by Justin Borevitz170
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[Bioc-devel] SNPscan -> SNPchip
... Hi Rob/Ingo just checking out your SNPchip package and clearly getting Copy Number Variation (CNV)and SNP calls together from genomic DNA hyb data is crucial going forward. We and others have developed SNP/tiling arrays for Arabidopsis and yeast and will hyb genomic DNA to genotype known SNPs/CNVs A ...
snp annotation yeast biobase snpchip written 12.6 years ago by Justin Borevitz170 • updated 12.6 years ago by Rob Scharpf240
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Spatial Correction
... It is adhoc and I?ve only thought a little about how to do regional correction more systematically (the way field studies correct for wet/soil spots locally effecting growth). Something like the xy pos of the feature is in the model for differential expression. This would be quite computational an ...
snp normalization affy oligo written 12.6 years ago by Justin Borevitz170 • updated 12.6 years ago by Matthew Lyon120
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Comment: C: genotyping RLMM probe level model?
... 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 i ...
written 12.7 years ago by Justin Borevitz170
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genotyping RLMM probe level model?
... 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' Su ...
snp probe rlmm written 12.7 years ago by Justin Borevitz170 • updated 12.7 years ago by Benilton Carvalho4.3k
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Answer: A: athPkgBuilder data source :missing probesets
... Hi We have re-annotated the ath1 probes with the V6 annotation for Arabidopsis. You can find it here http://naturalvariation.org/methods/ath1V6anno.RData in this probe setup 25mers with multiple gene matches are excluded.. We use probe level modeling for gene expression estimates. This is likely ...
written 12.8 years ago by Justin Borevitz170
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Answer: A: Communicating gene-probe relationships to sam
... An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20060508/ 89d0e21b/attachment.pl ...
written 13.1 years ago by Justin Borevitz170
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makecdfenv, bg.correct
... Hi Ben and BioC group, We've been doing many DNA hybridizations experiments to expression and tiling arrays and to call polymorphisms (SFPs and larger insertion/deletions). The bg.correct assumes a normal at the low end for scanner noise and an exponential for the signal of RNA. With DNA hybridiza ...
affy makecdfenv written 13.1 years ago by Justin Borevitz170
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SNPgenotyping
... An embedded and charset-unspecified text was scrubbed... Name: not available Url: https://stat.ethz.ch/pipermail/bioconductor/attachments/20060216/ 97042d1c/attachment.pl ...
written 13.3 years ago by Justin Borevitz170
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Answer: A: Affy Exon Array Analysis
... Yes this one limitation, the annotation for new arrays. So far we have done our own and can share with other Arabidopsis people if there is interest. We have developed methods for SFP (polymorphism detection) http://naturalvariation.org/sfp http://naturalvariation.org/methods and are toying with no ...
written 13.6 years ago by Justin Borevitz170

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