[BioC] Problem loading data for Agi4x44PreProcess

Bernal-Mizrachi, Leon lbernal at emory.edu
Tue Apr 28 14:14:54 CEST 2009

Dear Massimo,

Thanks for your replay.

I have 2 silly question and I apologize for it.

1. In the agilent platform there is several signals: gProcessedsignal,gMeanProcessedSignal,gMeanSignal and gBGMeanSignal. I understand that we can used the gMean and the gBGmean to substract the background. however what are those gProcessed and gMean?

2. If I have 18 samples and I want to creat the "targets.txt" data frame, how can I create it. In another words, looking at the vignette, how can I create a table such as:

FileName              Treatment GErep Subject Array
Ast Ast.txt st             1               A            1
Bst Bst.txt st              1               B            1
Aunst Aunst.txt unst  2              A            1
Bunst Bunst.txt unst  2               B            1

or how can I load my data into one onlyl file that  I can call "targets" and that has only the whatever signal you suggest I could use from question 1?

Sorry for this probably elemental question, I am trying to troubleshoot this platform.

Thanks again

Leon Bernal-Mizrachi, MD
Assistant Professor, Hematology/Medical Oncology
Emory University School of Medicine
Winship Cancer Institute
1365 Clifton Rd NE, C-3005
Atlanta, GA 30322
Phone: 404-778-1839
Fax: 404-778-5520
Email: lbernal at emory.edu

Admin. Asst.
Erica Alston
Erica.alston at emoryhealthcare.org

From: Massimo Pinto [pintarello at gmail.com]
Sent: Monday, April 27, 2009 4:16 AM
To: Bernal-Mizrachi, Leon
Subject: Re: Problem loading data for Agi4x44PreProcess


you mau need to avoid calling the data() function as at the example. That function calls in a sample targets file from the bundle, and it will over-ride yours.

Massimo Pinto
Post Doctoral Research Fellow
Enrico Fermi Centre and Italian Public Health Research Institute (ISS), Rome

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