Hi Sean,

Thank you very much for your reply. We have 12 arrays, 6 for each condition.
If I understood correctly, you're suggesting to remove high variable genes
within group (can i use 0.2% < CV < 10% to fiter out these high variable
genes? ).  I don't know how large for "large n"? Is it reasonable to use 6
per group?

Can you suggest some literature on power calculation for microarray?  I am
having little experience with statistics.

Thanks again,

Regards,
Sharon

On 12/1/05, Sean Davis <sdavis2@mail.nih.gov> wrote:
>
> On 12/1/05 8:50 AM, "Sharon Anbu" <sharonanandhi@gmail.com> wrote:
>
> > Hi All,
> >
> > I am working with the Affy data set for which the max fold change is
> > around 1.7.  Most of the probesets have a fold change between 1.2 and
> > 1.5. I have done the standard data analysis procedure reccommanded by
> > many people in Bioconductor (starting with RMA extraction, difference
> > between 2-groups, t-test, p-val & corrected p-val etc). After doing
> > this, I have got only 20 significant genes, which has no biological
> > significance with the experiment.
>
> How many arrays have you run?  If you know that you are looking for fold
> changes of 1.2-1.7 (I'm not sure how you know which genes are true and
> showing these changes, but...), you will likely need a stable system
> (little
> biological variability within groups) or a "relatively" large n.  You
> could
> do a simple power calculation to determine what your power is to detect a
> difference between your two groups given a "typical" variance and with
> different numbers of slides.  If you have good power with the number of
> slides that you are using, then you may be seeing true negative
> results.  If
> not, then increasing the number of arrays might be a good bet.  All that
> said, if you have a set of genes that you are interested in, you could go
> directly from "fold-change" on the array (ignore statistics such as
> p-value
> altogether) and move directly to validation with PCR-based methods.
>
> Sean
>
>

	[[alternative HTML version deleted]]

