[BioC] Working with low abundance probesets !!

[Sharon Anbu]

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