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<http://www.ebi.ac.uk/microarray-as/aer/result?queryFor=PhysicalArrayDesign&aAccession=A%2DAGIL%2D11>
)
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
>>
>>        [[alternative HTML version deleted]]
>>
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>>
>
>

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