[BioC] agilent data format

[Sean Davis]

Weiwei Shi wrote:
> 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?). 

You will almost certainly need to communicate with the biologist that
did the arrays to determine the experimental design.

> 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?

I think the LogRatio is probably the ratio between Red and Green, but
there is not a way to tell here.  Have these files been manipulated in
excel or something?  Agilent files typically have a much larger number
of columns and have a 9-line header.  The (+)Pro25G-03 and (-)3xSLv1 are
controls.

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

If you have files like the one above, read.table will read them just
fine.  If you have actual Agilent files (which these are not, I don't
think), then the limma package will read them.

Sean