[BioC] read.maimages(limma) source="agilent" updated for 20-bitscanner?

[Coleman, Ilsa]

Dear John,
Yes, Feature Extraction combines the two scans into a single results
file. It turns out that the results file format had changed because when
our scanner was serviced the settings were changed.  I realize now that
I would have had to specify the column headings regardless of this issue
because I would like to use the median signal measurements and the
column definition in the read.maimages function in limma (I'm using
v2.16.4) source="agilent" is G = "gMeanSignal",Gb = "gBGMedianSignal", R
= "rMeanSignal", Rb = "rBGMedianSignal". 
Thanks for your quick reply and help,
Ilsa

-----Original Message-----
From: John Fernandes [mailto:jfernand at stanford.edu] 
Sent: Wednesday, February 04, 2009 4:10 PM
To: Coleman, Ilsa
Cc: Sean Davis
Subject: Re: [BioC] read.maimages(limma) source="agilent" updated for
20-bitscanner?

In my experience, the Agilent Feature Extraction software creates a
single data file by combining the high/low scans so you'd have one data
file regardless of whether you did a single scan or a high/low double
scan.  Are you using Agilent Feature Extraction on the tiffs generated
by the scanner?

John

--------------------------------------------------
From: "Sean Davis" <seandavi at gmail.com>
Sent: Wednesday, February 04, 2009 3:59 PM
To: "Coleman, Ilsa" <icoleman at fhcrc.org>
Cc: <bioconductor at stat.math.ethz.ch>
Subject: Re: [BioC] read.maimages(limma) source="agilent" updated for
20-bitscanner?

> On Wed, Feb 4, 2009 at 6:39 PM, Coleman, Ilsa <icoleman at 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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>
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