[BioC] Suggestions on Agilent gene expression data

[Sean Davis]

On Wed, Jun 11, 2008 at 7:43 PM, ss <affysnp at gmail.com> 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?

Hi, Allen.  You'll probably need to do some quality control and some
normalization.  The choice of ratio is arbitrary; you can always
invert it if it is more convenient to do so.  As for log2 or log, they
are equivalent to each other with the exception of a constant.  You
might look at the limma manual for some guidance on working with
two-color arrays.

Sean