[BioC] Spatial Correction

[Matthew Lyon]

f.y.i. when the model's done running i also combine the call for any probes 
overlapping by at least 18bp in groups of 3.

Thank You,

Matthew Lyon        UC  Riverside                    lab (951) 827-4736
Ph.D. Student        B O T A N Y                new c.p. (951) 941-5554
                   Citrus Genomics                    apt (951) 328-9930
http: // int - citrusgenomics . org /           messengers: ptrifoliata
mattlyon at mattlyon.com ptrifoliata at hotmail.com mlyon003 at student.ucr.edu




>From: "Matthew Lyon" <ptrifoliata at hotmail.com>
>To: borevitz at uchicago.edu
>CC: bioconductor at stat.math.ethz.ch
>Subject: Re: [BioC] Spatial Correction
>Date: Sat, 14 Oct 2006 13:11:49 -0700
>
>Cool can u give us the form of the linear model?
>
>-----
>Justin Borevitz
>http://naturalsystems.org/lab
>
>-->
>
>sure. it's a multi-term model (engineering-kludge), where degrees of 
>freedom suffer and statistical validity is not the goal, just polishing the 
>data is. it’s designed to call a single chip’d progeny with respect to the 
>parents, run per probe:
>
>y_call=  B0
>+ B1*X_progenypm
>+ B2*X_progenymm
>+ B3*X_highpm1
>+ B4*X_highpm2
>+ B5*X_highpm3
>+ B6*X_lowpm1
>+ B7*X_lowpm2
>+ B8*X_lowpm3
>+ B9*X_highmm1
>+ B10*X_highmm2
>+ B11*X_highmm3
>+ B12*X_lowmm1
>+ B13*X_lowmm2
>+ B14*X_lowmm3
>- B15*X_gcp
>- B16*X_tmp
>- B17*X_ngp
>- B18*X_xpos < - these are the two you’re interested in.
>- B19*X_ypos < -
>
>o where y is a borevitizian sfp-call using a non-permed t-test, empirically 
>set to force ‘polymorphisms’ on about 10% of the chip (oversplitting)
>o where the perfect match probes, mismatch probes, two parents, and progeny 
>are in the named terms, with the parents always ordered high-to-low (hence, 
>high, low)
>o where the gcp, tmp, ngp, xpos, and ypos are build with + in the sign, 
>then the sign is flipped at evaluation time.
>o where the output is then split empirically, as well.
>
>Thank You,
>
>Matthew Lyon        UC  Riverside                    lab (951) 827-4736
>Ph.D. Student        B O T A N Y                new c.p. (951) 941-5554
>                   Citrus Genomics                    apt (951) 328-9930
>http: // int - citrusgenomics . org /           messengers: ptrifoliata
>mattlyon at mattlyon.com ptrifoliata at hotmail.com mlyon003 at student.ucr.edu
>


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