[BioC] Spatial Correction
Matthew Lyon
ptrifoliata at hotmail.com
Sat Oct 14 21:55:32 CEST 2006
heh. we're often on the same wavelength it seems. i'm already doing this x-y
slope across the whole 'field' thing a bit in my linear modeling work,
inspired by borevitz's occosional inclusion of probe set id #'s as null-
components when checking stats/models, instead i input them as x and y's,
split up as terms in a model for calling the chip. i have to say: the
coeffiecients sure don't look like they matter much? i think i'm going to
leave it in as an engineering/q.a. thing, though.
e.g. coeffiecients for a model that slams everything down to
snp/sfp-calls/copy-number (sorry no anova, sigs, or f-test output on these
runs):
statcutoffs tcut: 12.236 high: 21.2475972466423 low: 16.5098342910872
built model of 42317 points, spread as transects across the chip.
constant 2.06606598216225
---
progenypm 0.0813258560574814
progenymm -0.00294383026705664
highpm1 -0.0486924459388655
highpm2 -0.0365650706946507
highpm3 -0.046313242027037
lowpm1 0.0181522513255337
lowpm2 0.0161600597386146
lowpm3 0.0160355165311527
highmm1 -0.0110724545083531
highmm2 -0.00663396018469053
highmm3 -0.0116972092671024
lowmm1 0.00326259465264771
lowmm2 0.00567155215296054
lowmm3 0.0013044918026059
-- gc content:
gcp (sign gets flipped) -0.00101239058730091
-- nearest neighbor temperature:
tmp (sign gets flipped) 0.00153804487609968
-- number of G's in probe (the c's get labeled):
ngp (sign gets flipped) 0.00554060155127831
---
xpos (sign gets flipped) -2.14773325615418e-05 <-- x 10 to the minus
5, that's not-so-much?
ypos (sign gets flipped) 6.94183011922954e-06
---
as far as abberant spot correction (real spatial correction by-zones) i'm
not doing this and am simply re-running the bad experiements - for some
reason a few of our chips have smudges that look like nike-swooths on them
where the hybridization is killed significantly.
---
as far as labeling for dna is concerned i would die to see someone compare
end-transferase and random label inclusion (perhaps in the same hyb mix as
different fluorophore colors on a multi-channel scanner?). is there any work
/ pubs out there that do this?
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: "Justin Borevitz" <borevitz at uchicago.edu>
>To: "'Michael Gore'" <mag87 at cornell.edu>
>CC: Ben Bolstad <bolstad at stat.berkeley.edu>, "'Bioconductor'"
><bioconductor at stat.math.ethz.ch>
>Subject: Re: [BioC] Spatial Correction
>Date: Sat, 14 Oct 2006 09:53:52 -0500
>
>It is adhoc and Ive 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 and normalization wouldnt come in the standard way either.
>
>So bg.correct from RMA is not spatial correction. It doesnt consider the
>XY
>pos. It does a global per array correction for each array, but assumes
>normal noise and exponential RNA signal. Ben Bolstad was going to model
>normal noise and normal signal for DNA, but I dont think he has done it
>yet, no pressure Ben... We might be in lower demand however SNP arrays
>might benefit tremendously from normal/normal. SNP arrays do have their own
>correction method with the oligo package though and Im not sure if anyone
>tired this for RNA or if it makes sense even.
>
>Yes quantile normalization is the next step and good luck with the maize
>SFPs, if you use whole genome random labeling I guess it will be noisily
>but
>possible with enough replicates. The deletions sure should be. Otherwise
>a
>complexity reduction eg AFPL etc might help, see our Barley paper
>http://genomebiology.com/2005/6/6/r54
>
>
>-----
>Justin Borevitz
>http://naturalsystems.org/lab
>________________________________________
>From: Michael Gore [mailto:mag87 at cornell.edu]
>Sent: Friday, October 13, 2006 6:08 PM
>To: 'Justin Borevitz'
>Subject: Spatial Correction
>
>Hi Justin,
>
>I have a quick question for you. How does one determine the appropriate
>array size and filter size for spatial correction?
>
>Is spatial correction comparable to RMA, followed by Quantiles?
>
>Right now, we are doing SFP with the Affy Maize GeneChip.
>
>Thanks,
>
>Mike
>
>
>library(affy)
>read.cel <- function(cel.file, cel.image = F, spatial.correct=T, median=F,
> array.size = 712, filter.size = 51,
>jpeg.save=T){
>
>
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