[BioC] agilent data format

Weiwei Shi helprhelp at gmail.com
Thu Jun 14 21:13:46 CEST 2007

Dear Listers:

This is my first time to look at Agilent's data for one of my research
on cross-platform issue; So this is very newbie's question:

one example is like this:
two files with cy3_50mg_6h_Rat_3125.txt and cy5_50my_6h_Rat_3125.txt.
I believe one of them must be control but not sure which one (is there
a tradition to use cy5 as control?). One of the dataset's format looks
like this:

ProbeName	GeneName	LogRatio	PValueLogRatio
(+)Pro25G-03	Pro25G	-4.92E-01	9.04E-16
(-)3xSLv1	NegativeControl	0.00E+00	1.00E+00
A_43_P21252	CB546590	1.64E-02	7.96E-01
A_42_P534203	272585_Rn	-8.69E-03	9.16E-01
A_43_P22195	CB547437	4.77E-02	4.90E-01
A_43_P16421	AA964066	-9.25E-04	9.87E-01
(+)Pro25G-02	Pro25G	-1.58E+00	1.10E-33
A_43_P13118	NM_130424	4.12E-02	4.68E-01
A_43_P19445	CB605581	-1.74E-03	9.93E-01
A_43_P11302	BQ206007	-9.17E-02	1.56E-01
A_43_P22361	AA964019	-1.31E-01	5.83E-01
A_43_P10152	BF420136	6.54E-02	4.11E-01
A_42_P573643	234509_Rn	5.87E-02	2.43E-01

I assume the LogRatio is the signal against background? But what is
(+)Pro25G-03 or (-)3xSLv1?

btw, are there some packages to read this type of data format?


Weiwei Shi, Ph.D
Research Scientist
GeneGO, Inc.

"Did you always know?"
"No, I did not. But I believed..."
---Matrix III

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