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.  Now, I am thinking of trying other measures instead of
difference between groups. What kinds of measures I should try?
Is there any method addressing the issue of detecting low abundance
probesets in Bioconductor?

Thanks in Advance.

Regards,
Sharon

	[[alternative HTML version deleted]]

