[BioC] Spatial Correction

[Justin Borevitz]

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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