[BioC] Duplicate probesets in mouse4302

[Henrik Bengtsson]

Hi.

On Mon, Feb 2, 2009 at 9:28 AM, Paul Geeleher <paulgeeleher at gmail.com> wrote:
> 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.

Microarray studies are almost all about comparing signals to a
reference.  The reference might be the "normal" in a tumor/normal
pair, another sample, or a pool of many samples.  The idea is that by
taking ratios toward a reference, then gene/probeset/probe/locus/...
specific scale factors ("affinities") cancels out.  Your "expression
levels" are not relative to a reference and for this reason contain
traces of such (unknown) affinities.  The different "expression
levels" probably carry quite different affinities, and are therefore
not comparable.  This is why "expression levels" on their own does not
make sense.  However, when you say there is "some correlation in the
change", you are comparing to a common reference (time point or
relative to each other; not sure how you did it).  Actually, I guess
all measurements in Universe require some reference in order to make
any sense.

My $.02

/Henrik

>
> 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
>
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