Dear Sean,
Thanks for your quick reply.  After more investigation, I found out what
the problem was.  It turns out that prior to the switch to 20-bit scans
(so nothing to do with that) our scanner was upgraded and all of the
settings were changed.  At the time the files switched to a different
format which does not include some of the columns the default
read.maimages function uses for source="agilent" (specificially, the
files now completely lack "gMeanSignal" and "rMeanSignal" values.)  I
prefer to use the gMedianSignal and rMedianSignal anyway and will
continue to do so by specifying the column definition as you suggested.
(I was previously using a different program for processing array data
and I am switching over to limma so thanks for your help, it's much
appreciated!
Ilsa
 
________________________________

From: Sean Davis [mailto:seandavi@gmail.com] 
Sent: Wednesday, February 04, 2009 4:00 PM
To: Coleman, Ilsa
Cc: bioconductor@stat.math.ethz.ch
Subject: Re: [BioC] read.maimages(limma) source="agilent" updated for
20-bit scanner?




On Wed, Feb 4, 2009 at 6:39 PM, Coleman, Ilsa <icoleman@fhcrc.org>
wrote:


	Hi,
	I can read in 2-color Agilent data from 16-bit scans (Agilent
Technologies Scanner G2505B) using read.maimages(limma) source="agilent"
but for some reason cannot read in data files from 20-bit scans (Agilent
Technologies Scanner G2505C).  This probably has to do with the fact
that the 20-bit scans no longer require two scans (low and high) so
there are fewer data columns in these files.  Has anyone else had this
problem and is there a plan to update the read.maimages(limma) function?
	


Hi, Ilsa.  You can specify the columns to read using read.maimages.  See
the help page for a great deal of detail.

Sean




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