Hi Sean,

Thanks a lot! The data we downloaded has already been normalized and
processed.
So I guess I can go ahead without further quality control. My question then
is that
if I want to utilize some other tools or softwares for higher level
analysis, should I use
ratio, or log2(ratio) or Log(ratio)? Or it does not matter at all?

Best,
     Allen



On Wed, Jun 11, 2008 at 10:01 PM, Sean Davis <sdavis2@mail.nih.gov> wrote:

> On Wed, Jun 11, 2008 at 7:43 PM, ss <affysnp@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
>

	[[alternative HTML version deleted]]

