[BioC] Duplicate probesets in mouse4302

[Paul Geeleher]

I'm analyzing a dataset from a mouse4302 array and I'm interested in
looking at the expression levels of the various caspases over the 8
timepoints of the experiment. The thing is the mouse4302.db annotation
package seems to, in many cases, map several different probesets to
the same genename. For example 3 genesets have genename caspase 3; 3
genesets are called caspase 9 and there are duplicates for caspases 8,
14, 7 and more.

The next problem is that there is in most cases very little
correlation between the expression levels of the different genesets
which are meant to represent the same thing.

For example, caspase 3 as approximate average log expression levels of
5.2, 9.1 and 10.2 in the different probesets, which seem hugely
different. There does however seem to be some correlation in the
change of expression level over the time course.

My question is basically first, why is this the case? And second, how
should I deal with it to get some idea what is happening biologically?

-- 
Paul Geeleher
School of Mathematics, Statistics and Applied Mathematics
National University of Ireland
Galway
Ireland