As you said yourself, these are processed intensities, so how should  
we know what to do with them. It does not come out of Agilents software.

But given these columns names I guess that
  - Ratio is equal to Intensity 1 / Intensity 2 (or vice verse)
  - Log(Ratio) is the logarithm of Ratio, check yourself to see what  
base they are using. My guess is either 2 or 10 but it could be e
  - I have no idea what Fold Change is, my guess would be that it is  
the same as Ratio
  - P value and log(error) are some kind of statistics associated with  
the hypothesis that intensity 1 is equal to intensity 2
  - It is a two colour array.

I would use Log(Ratio), checking to see what base it is in.

Perhaps you can check out the raw files (which are probably Agilent  
files) and figure out what the columns are. They could correspond to  
something like gPorcessedSignal/rProcessedSignal

Kasper

On Jun 13, 2008, at 8:12 PM, ss wrote:

> Just to follow up a bit, there are 7 corresponding columns for each  
> sample.
> For instance, for the 1st array, they are:
>
>
> MBA: US14702370_16012391010920_S01_A01/Log(Ratio)
> MBA: US14702370_16012391010920_S01_A01/Ratio
> MBA: US14702370_16012391010920_S01_A01/Fold Change
> MBA: US14702370_16012391010920_S01_A01/Log(Error)
> MBA: US14702370_16012391010920_S01_A01/P-Value
> MBA: US14702370_16012391010920_S01_A01/Intensity 1
> MBA: US14702370_16012391010920_S01_A01/Intensity 2
>
> I figure I should use Ratio which is Intensity2/Intensity1 for  
> further analysis.
> I really wish I could get started with raw data but I just dont know  
> whether
> there is some packages for Agilent data.
>
> Allen
>
> On Fri, Jun 13, 2008 at 11:09 PM, ss <affysnp@gmail.com> wrote:
> Thanks Kasper. We downloaded the processed data under the
> accession number 'E-TABM-1' from ArrayExpress at http://www.ebi.ac.uk/microarray-as/aer/#ae-browse/ 
> q=E-TABM-1[2]
>
> So if you click 'E-TABM-1' and it says that:
>
> Array:
> Agilent Whole Human Genome Oligo Microarray [G4112A] (ť A-AGIL-11)
> I guess it is of Agilent format for sure. What does it seem strange to
> you?
>
> Allen
>
>
>
> On Fri, Jun 13, 2008 at 11:05 PM, Kasper Daniel Hansen <khansen@stat.berkeley.edu 
> > wrote:
> This does not look at all like an Agilent data file from Feature  
> Extractor. I suggest you contact your collaborators and get an idea  
> about what you should use.
>
> Kasper
>
>
> On Jun 11, 2008, at 4:43 PM, ss wrote:
>
> Dear all,
>
> For whom is familiar with Agilent gene expression data, I would like  
> to
> ask help.
>
> We recently received some Agilent gene expression data from our
> collaborators. For individual sample, there are 7 corresponding  
> columns:
>
>  Unknown:Log(Ratio)  Unknown:Ratio  Unknown:Fold Change   
> Unknown:Log(Error)
> Unknown:P-Value  Unknown:Intensity 1  Unknown:Intensity 2
> It seems that Ratio= Intensity1/Intensity2. I wonder whether I  
> should use
> log2(Ratio) or Log(Ratio) or just Ratio for further analysis.  
> Besides, why
> should Ratio be calculated as Intensity1/Intensity2 instead of
> Intensity2/Intensity1?
>
> Thank you very much for your help in advance!
>
> Sincerely,
>     Allen
>
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