[BioC] Spatial Correction

[Rafael A. Irizarry]

all robust summaries ive used: li and wong's algo, median polish and rlm
within RMA appear to find these spatial artifacts as outliers (under a
typical definition of an outlier). an easy way to see this is to make an
image plot of the absolute value of the residuals from the model fit.



On Sun, 8 Jun 2003, Justin Borevitz wrote:

> Hi all great to be part of a highly active/responsive group!
> 
> Has anyone else thought about spatial correction for affy arrays?  Charles
> Berry and I have done some simple corrections using sliding windows, see
> Figure 1. http://www.genome.org/cgi/content/full/13/3/513/F1 or
> http://naturalvariation.org/sfp/Borevitz_etal_2003_GR.pdf  I know dCHIP can
> mask out scratches.  Could there be something that would take advantage of
> multichip analysis, kind of like quantile normalization but that would
> consider the data in its original image form (rectangular matrix of feature
> intensities)?  I often see smudges on arrays where useful data is below that
> needs to be locally corrected for.
> 
> FYI I have the cdf package for the Arabidopsis ATH1 array here.
> 
> http://natural.salk.edu/ath1121501cdf.tar.gz   ## source
> http://natural.salk.edu/ath1121501cdf.zip   ## win32
> 
> original cdf from affy
> http://natural.salk.edu/Ath1.cdf.zip
> 
> Justin
> http://naturalvariation.org 
> 
> -----Original Message-----
> From: bioconductor-bounces at stat.math.ethz.ch
> [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Johannes Hüsing
> Sent: Saturday, June 07, 2003 1:47 AM
> To: Tapan Mehta
> Cc: bioconductor at stat.math.ethz.ch; John Zhang
> Subject: Re: [BioC] Bioconductor commands in Unix online documentation
> request
> 
> Tapan Mehta <tapmehta at yahoo.com> [Sat, Jun 07, 2003 at 09:07:27AM CEST]:
> > Thank you all for the help. It would be nice if I
> > could know about some documentation for R/bioconductor
> > commands that can be used in Unix through command
> > line.
> 
> There is no direct interface to internal R commands from any shell I
> know, if you mean that.
> 
> You can always type 
> 
> echo "sqrt(2)" | R CMD BATCH
> 
> and then inspect .R.Rout, which is the closest thing to what I think you
> mean.
> 
> Greetings
> 
> 
> Johannes
> -- 
> Johannes Hüsing   There is something fascinating about science. One gets
> hannes at ruhrau.de  such wholesale returns of conjecture from such a 
>                   trifling investment of fact.                Mark Twain
> 
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