[BioC] Differential Gene Expression Analyses

[Avoks AO]

Hi,

Is it possible to have a single protocol to analyze differential gene
expression for experiments of different design? A dataset like GDS3715
in GEO, for example, has both levels and sub-levels (agents).  One of
the levels, say insulin resistant, is divided into sub-levels treated
and untreated samples. GDS162 on the other hand is grouped into just
two levels(no sub-levels). Running res = sam(gdseset,
gdseset$disease.state)works fine for data with just levels.  res =
sam(gdseset, gdseset$agent) understandably groups everything into 2
classes, treated and untreated, which doesn't make much sense, to me
anyway. And using res = sam(gdseset, gdseset$disease.state$agent)
doesn't work. Is there a way to possibly identify, correctly assign
and pair up such sub-level data if and when the script comes across
it?

Thanks.

-Avoks