[BioC] Spatial Correction

Matthew Lyon ptrifoliata at hotmail.com
Sat Oct 14 22:11:49 CEST 2006

Cool can u give us the form of the linear model?

Justin Borevitz


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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