[BioC] targets frame

Giusy Della Gatta Gatta at icg.cpmc.columbia.edu
Tue Dec 16 21:12:41 CET 2008

Thank you Kasper,
I uploaded the file and I was trying to make the RG list but I got
this message:

> library (limma)
> targets <- readTargets("target_frame_barc.txt")
> RG <-read.maimages (targets$FileName, source="agilent")

Error in read.maimages(targets$FileName, source = "agilent") : 
  Must specify input files

The file are in the same working directory and they are coming from
agilent analysis, have I to specify something else?

Thank you

-----Original Message-----
From: Kasper Daniel Hansen [mailto:khansen at stat.berkeley.edu]
Sent: Tue 12/16/2008 12:08 PM
To: Giusy Della Gatta
Cc: bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] targets frame
In the filename give it the name of the actual output file from  
Feature Extractor. That should be a big textfile, perhaps 30MB or more.

Read the limma's Users Guide, see priscilla's email from today/ 
yesterday. She had almost the same question.


On Dec 16, 2008, at 8:15 , Giusy Della Gatta wrote:

> Hi everybody,
> I am a beginner in the use of R for microarray normalization.
> I have Agilent two color microarray data, so I was thinking to use
> the Bioconductor LIMMA package to normalize my microarray
> by using loess method.
> In the first step there is the composition of a targets file.
> I did not undestand which kind of Agilent files I have to specify:
> they are asking to put in the filename column "the name of the image  
> analysis
> output file" , which are the Agilent image analysis
> output file?
> Anybody can help me?
> Thank you
> Giu
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